INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(69581, 1999, 'bio', 'KIND-a non-redundant protein database', 'Kallberg, Y|Persson, B', 'Department of Medical Biochemistry and Biophysics, Karolinska Institutet,S-171 77 Stockholm, Sweden. yvonne.kallberg@mbb.ki.se|Department of Medical Biochemistry and Biophysics, Karolinska Institutet,S-171 77 Stockholm, Sweden. yvonne.kallberg@mbb.ki.se', 'Sweden|Sweden', 0, 'Algorithms|Databases, Factual|Open Reading Frames|Proteins|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/15.3.260', '10222415', 'KIND (Karolinska Institutet Nonredundant Database) is a protein database where identical sequences, both full length and partial, have been removed. The database contains nearly 274 900 sequences, half of which originate from the protein sequence databases Swissprot and PIR, while the other half come from translated open reading frames in GenPept and TrEMBL.'),
(69582, 1999, 'bio', 'WWW access to the SYSTERS protein sequence cluster set', 'Krause, A|Nicodème, P|Bornberg-Bauer, E|Rehmsmeier, M|Vingron, M', 'Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, INF 280, D-69120 Heidelberg, Germany. A.Krause@DKFZ-Heidelberg.de|Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, INF 280, D-69120 Heidelberg, Germany. A.Krause@DKFZ-Heidelberg.de|Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, INF 280, D-69120 Heidelberg, Germany. A.Krause@DKFZ-Heidelberg.de|Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, INF 280, D-69120 Heidelberg, Germany. A.Krause@DKFZ-Heidelberg.de|Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, INF 280, D-69120 Heidelberg, Germany. A.Krause@DKFZ-Heidelberg.de', 'Germany|Germany|Germany|Germany|Germany', 11, 'Algorithms|Amino Acid Sequence|Animals|Databases, Factual|Humans|Internet|Molecular Sequence Data|Proteins|Sequence Alignment|Sequence Homology, Amino Acid', 'Journal Article', '10.1093/bioinformatics/15.3.262', '10222416', 'We present a Web server where the SYSTERS cluster set of the non-redundant protein database consisting of sequences from SWISS-PROT and PIR is being made available for querying and browsing. The cluster set can be searched with a new sequence using the SSMAL search tool. Additionally, a multiple alignment is generated for each cluster and annotated with domain information from the Pfam protein family database.'),
(69583, 1999, 'bio', 'DNA-binding requirements of the yeast protein Rap1p as selected in silico from ribosomal protein gene promoter sequences', 'Lascaris, R F|Mager, W H|Planta, R J', 'Department of Biochemistry and Molecular Biology, IMBW, Biocentrum Amsterdam, Vrije Universiteit, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.|Department of Biochemistry and Molecular Biology, IMBW, Biocentrum Amsterdam, Vrije Universiteit, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.|Department of Biochemistry and Molecular Biology, IMBW, Biocentrum Amsterdam, Vrije Universiteit, de Boelelaan 1083, 1081 HV Amsterdam, The Netherlands.', 'Netherlands|Netherlands|Netherlands', 41, 'Base Sequence|Binding Sites|DNA, Fungal|DNA-Binding Proteins|Databases, Factual|Fungal Proteins|Genome, Fungal|Molecular Sequence Data|Oligodeoxyribonucleotides|Promoter Regions, Genetic|Repressor Proteins|Ribosomal Proteins|Saccharomyces cerevisiae|Saccharomyces cerevisiae Proteins|Telomere|Telomere-Binding Proteins', 'Journal Article', '10.1093/bioinformatics/15.4.267', '10320394', 'High-level transcriptional activation of most ribosomal protein (rp) genes in Saccharomyces cerevisiae is promoted by the global DNA-binding factor Rap1p. The creation of the complete database of yeast rp gene promoter sequences enabled us to develop a computational selection strategy aimed at acquiring detailed information concerning the DNA-binding specificity of Rap1p.'),
(69584, 1999, 'bio', 'Revealing hidden interval graph structure in STS-content data', 'Harley, E|Bonner, A|Goodman, N', 'Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 1A4. eharley@cs.toronto.edu|Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 1A4. eharley@cs.toronto.edu|Department of Computer Science, University of Toronto, Toronto, Ontario, Canada M5S 1A4. eharley@cs.toronto.edu', 'Canada|Canada|Canada', 6, 'Algorithms|Contig Mapping|Databases, Factual|Humans|Neural Networks (Computer)|Sequence Tagged Sites', 'Journal Article', '10.1093/bioinformatics/15.4.278', '10320395', 'STS-content data for genomic mapping contain numerous errors and anomalies resulting in cross-links among distant regions of the genome. Identification of contigs within the data is an important and difficult problem.'),
(69585, 1999, 'bio', 'A vector-based method for drawing RNA secondary structure', 'Han, K|Kim, D|Kim, H J', 'Department of Automation Engineering, Inha University, Inchon 402-751 and College of Pharmacy, Chung Ang University, Seoul 156-756, South Korea. khan@inha.ac.kr|Department of Automation Engineering, Inha University, Inchon 402-751 and College of Pharmacy, Chung Ang University, Seoul 156-756, South Korea. khan@inha.ac.kr|Department of Automation Engineering, Inha University, Inchon 402-751 and College of Pharmacy, Chung Ang University, Seoul 156-756, South Korea. khan@inha.ac.kr', '-|-|-', 0, 'Algorithms|Animals|Computer Simulation|Models, Molecular|Nucleic Acid Conformation|RNA|RNA, Protozoan|Software|Tetrahymena', 'Journal Article', '10.1093/bioinformatics/15.4.286', '10320396', 'To produce a polygonal display of RNA secondary structure with minimal overlap and distortion of structural elements, with minimal search for positioning them, and with minimal user intervention.'),
(69586, 1999, 'bio', 'Calign: aligning sequences with restricted affine gap penalties', 'Chao, K M', 'Department of Computer Science and Information Management, Providence University, Shalu, Taichung, Taiwan. kmchao@csim.pu.edu.tw', '-', 2, 'Algorithms|Humans|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/15.4.298', '10320397', 'Given a genomic DNA sequence, it is still an open problem to determine its coding regions, i.e. the region consisting of exons and introns. The comparison of cDNA and genomic DNA helps the understanding of coding regions. For such an application, it might be adequate to use the restricted affine gap penalties which penalize long gaps with a constant penalty.'),
(69587, 1999, 'bio', 'ESPript: analysis of multiple sequence alignments in PostScript', 'Gouet, P|Courcelle, E|Stuart, D I|Métoz, F', 'Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK. gouet@ipbs.fr|Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK. gouet@ipbs.fr|Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK. gouet@ipbs.fr|Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK. gouet@ipbs.fr', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom', 0, 'Amino Acid Sequence|Molecular Sequence Data|Protein Structure, Secondary|Proteins|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/15.4.305', '10320398', 'The program ESPript (Easy Sequencing in PostScript) allows the rapid visualization, via PostScript output, of sequences aligned with popular programs such as CLUSTAL-W or GCG PILEUP. It can read secondary structure files (such as that created by the program DSSP) to produce a synthesis of both sequence and structural information.'),
(69588, 1999, 'bio', 'DINAMO: interactive protein alignment and model building', 'Bentz, J|Baucom, A|Hansen, M|Gregoret, L', 'Departments of Biology, Computer Science and Chemistry & Biochemistry, University of California, Santa Cruz, CA 95064, USA.|Departments of Biology, Computer Science and Chemistry & Biochemistry, University of California, Santa Cruz, CA 95064, USA.|Departments of Biology, Computer Science and Chemistry & Biochemistry, University of California, Santa Cruz, CA 95064, USA.|Departments of Biology, Computer Science and Chemistry & Biochemistry, University of California, Santa Cruz, CA 95064, USA.', 'United States|United States|United States|United States', 3, 'Amino Acid Sequence|Computer Graphics|Computer Simulation|Models, Molecular|Molecular Sequence Data|Proteins|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/15.4.309', '10320399', 'To facilitate the process of structure prediction by both comparative modeling and fold recognition, we describe DINAMO, an interactive protein alignment building and model evaluation tool that dynamically couples a multiple sequence alignment editor to a molecular graphics display. DINAMO allows the user to optimize the alignment and model to satisfy the known heuristics of protein structure by means of a set of analysis tools. The analysis tools return information to both the alignment editor and graphics model in the form of visual cues (color, shape), allowing for rapid evaluation. Several analysis tools may be employed, including residue conservation, residue properties (charge, hydrophobicity, volume), residue environmental preference, and secondary structure propensity.'),
(69589, 1999, 'bio', 'Motif-based searching in TOPS protein topology databases', 'Gilbert, D|Westhead, D|Nagano, N|Thornton, J', 'Department of Computer Science, City University, London EC1V 0HB, UK. drg@cs.city.ac.uk|Department of Computer Science, City University, London EC1V 0HB, UK. drg@cs.city.ac.uk|Department of Computer Science, City University, London EC1V 0HB, UK. drg@cs.city.ac.uk|Department of Computer Science, City University, London EC1V 0HB, UK. drg@cs.city.ac.uk', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom', 0, 'Algorithms|Database Management Systems|Databases, Factual|Information Storage and Retrieval|Programming Languages|Protein Conformation|Proteins', 'Journal Article', '10.1093/bioinformatics/15.4.317', '10320400', 'TOPS cartoons are a schematic ion of protein three-dimensional structures in two dimensions, and are used for understanding and manual comparison of protein folds. Recently, an algorithm that produces the cartoons automatically from protein structures has been devised and cartoons have been generated to represent all the structures in the structural databank. There is now a need to be able to define target topological patterns and to search the database for matching domains.'),
(69590, 1999, 'bio', 'Automated analysis of interatomic contacts in proteins', 'Sobolev, V|Sorokine, A|Prilusky, J|Abola, E E|Edelman, M', 'Department of Plant Sciences and Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel. lpsobol@weizmann.ac.il|Department of Plant Sciences and Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel. lpsobol@weizmann.ac.il|Department of Plant Sciences and Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel. lpsobol@weizmann.ac.il|Department of Plant Sciences and Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel. lpsobol@weizmann.ac.il|Department of Plant Sciences and Bioinformatics Unit, Weizmann Institute of Science, Rehovot, Israel. lpsobol@weizmann.ac.il', 'Israel|Israel|Israel|Israel|Israel', 0, 'Automation|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/15.4.327', '10320401', 'New software has been designed to assist the molecular biologist in understanding the structural consequences of modifying a ligand and/or protein.'),
(69591, 1999, 'bio', 'The Biopolymer Markup Language', 'Fenyö, D', 'Proteometrics, LLC, 38 W. 38th Street, New York, NY 10018, USA. bioml@proteometrics.com', 'United States', 35, 'Biopolymers|Computer Simulation|Models, Molecular|Programming Languages', 'Journal Article', '10.1093/bioinformatics/15.4.339', '10320402', 'An XML derived from a data model designed to be a hierarchical representation of an organism has been specified and a browser to use this language has been developed.'),
(69592, 1999, 'bio', 'MIAH: automatic alignment of eukaryotic SSU rRNAs', 'Thébault, P|Monestié, P|McGrath, A|Higgins, D G', 'Department of Biochemistry, University College, Cork, Ireland.|Department of Biochemistry, University College, Cork, Ireland.|Department of Biochemistry, University College, Cork, Ireland.|Department of Biochemistry, University College, Cork, Ireland.', 'Ireland|Ireland|Ireland|Ireland', 1, 'Automation|Eukaryotic Cells|RNA, Ribosomal|Sequence Alignment|Sequence Analysis, RNA|Software', 'Journal Article', '10.1093/bioinformatics/15.4.341', '10320403', 'MIAH is a WWW server for the automatic alignment of new eukaryotic SSU rRNA sequences to an existing alignment of 1500 sequences.'),
(69593, 1999, 'bio', 'The domain-server: direct prediction of protein domain-homologies from BLAST search', 'Murvai, J|Vlahovicek, K|Barta, E|Parthasarathy, S|Hegyi, H|Pfeiffer, F|Pongor, S', 'International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy.|International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy.|International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy.|International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy.|International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy.|International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy.|International Centre for Genetic Engineering and Biotechnology, 34012 Trieste, Italy.', 'Italy|Italy|Italy|Italy|Italy|Italy|Italy', 0, 'Algorithms|Humans|Information Storage and Retrieval|Protein Conformation|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/15.4.343', '10320404', 'A WWW server for protein domain homology prediction, based on BLAST search and a simple data-mining algorithm (Hegyi,H. and Pongor,S. (1993) Comput. Appl. Biosci., 9, 371-372), was constructed providing a tabulated list and a graphic plot of similarities.'),
(69594, 1999, 'bio', 'CoPE: a collaborative pedigree drawing environment', 'Brun-Samarcq, L|Gallina, S|Philippi, A|Demenais, F|Vaysseix, G|Barillot, E', 'GIS Infobiogen, 7 rue Guy Môquet, BP 8, 94801 Villejuif cedex, France. cope@infobiogen.fr|GIS Infobiogen, 7 rue Guy Môquet, BP 8, 94801 Villejuif cedex, France. cope@infobiogen.fr|GIS Infobiogen, 7 rue Guy Môquet, BP 8, 94801 Villejuif cedex, France. cope@infobiogen.fr|GIS Infobiogen, 7 rue Guy Môquet, BP 8, 94801 Villejuif cedex, France. cope@infobiogen.fr|GIS Infobiogen, 7 rue Guy Môquet, BP 8, 94801 Villejuif cedex, France. cope@infobiogen.fr|GIS Infobiogen, 7 rue Guy Môquet, BP 8, 94801 Villejuif cedex, France. cope@infobiogen.fr', 'France|France|France|France|France|France', 4, 'Pedigree|Software', 'Journal Article', '10.1093/bioinformatics/15.4.345', '10320405', 'We developed a collaborative pedigree environment called CoPE. This environment includes a Java program for drawing pedigrees and a standardized system for pedigree storage. Unlike other existing pedigree programs, this software is particularly intended for epidemiologists in the sense that it allows customized automatic drawing of large numbers of pedigrees and remote and distributed consultation of pedigrees.'),
(69595, 1999, 'bio', 'Wrapping SRS with CORBA: from textual data to distributed objects', 'Coupaye, T', 'IMAG LSR, University of Grenoble, Actimart, Bat. 8, Avenue de Vignate, 38610 Gieres, France. Thierry.Coupaye@imag.fr', 'France', 6, 'Computer Systems|Database Management Systems|Databases, Factual|Information Storage and Retrieval|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/15.4.333', '10320658', 'Biological data come in very different shapes. Databanks are maintained and used by distinct organizations. Text is the de facto Standard exchange format. The SRS system can integrate heterogeneous textual databanks but it was lacking a way to structure the extracted data.'),
(69596, 1998, 'bio', 'What we do not know about sequence analysis and sequence databases', 'Karp, P D', 'IMAG LSR, University of Grenoble, Actimart, Bat. 8, Avenue de Vignate, 38610 Gieres, France. Thierry.Coupaye@imag.fr', 'France', 95, 'Databases, Factual|Sequence Analysis', 'Editorial', '10.1093/bioinformatics/14.9.753', '10366280', '-'),
(69597, 1999, 'bio', 'ProbeDesigner: for the design of probesets for branched DNA (bDNA) signal amplification assays', 'Bushnell, S|Budde, J|Catino, T|Cole, J|Derti, A|Kelso, R|Collins, M L|Molino, G|Sheridan, P|Monahan, J|Urdea, M', 'Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.|Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.|Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.|Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.|Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.|Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.|Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.|Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.|Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.|Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.|Chiron Diagnostics, 333 Coney Street, Walpole, MA 02032, USA.', 'United States|United States|United States|United States|United States|United States|United States|United States|United States|United States|United States', 27, 'Animals|DNA|DNA Probes|Electronic Data Processing|Humans|Nucleic Acid Amplification Techniques|Nucleic Acid Hybridization|Software', 'Journal Article', '10.1093/bioinformatics/15.5.348', '10366654', 'The sensitivity and specificity of branched DNA (bDNA) assays are derived in part through the judicious design of the capture and label extender probes. To minimize non-specific hybridization (NSH) events, which elevate assay background, candidate probes must be computer screened for complementarity with generic sequences present in the assay.'),
(69598, 1999, 'bio', 'Promoter20: for the recognition of PolII promoter sequences', 'Knudsen, S', 'Center for Biological Sequence Analysis, The Technical University of Denmark, DK-2800 Lyngby, Denmark. steen@cbs.dtu.dk', 'Denmark', 232, 'Algorithms|Animals|Binding Sites|Humans|Neural Networks (Computer)|Promoter Regions, Genetic|RNA Polymerase II|Software|TATA Box|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/15.5.356', '10366655', 'A new approach to the prediction of eukaryotic PolII promoters from DNA sequence takes advantage of a combination of elements similar to neural networks and genetic algorithms to recognize a set of discrete subpatterns with variable separation as one pattern: a promoter. The neural networks use as input a small window of DNA sequence, as well as the output of other neural networks. Through the use of genetic algorithms, the weights in the neural networks are optimized to discriminate maximally between promoters and non-promoters.'),
(69599, 1999, 'bio', 'Interpolated markov chains for eukaryotic promoter recognition', 'Ohler, U|Harbeck, S|Niemann, H|Nöth, E|Reese, M G', 'University of Erlangen-Nuremberg, Martensstrasse 3, D-91058 Erlangen, Germany. ohler@informatik.uni-erlangen.de|University of Erlangen-Nuremberg, Martensstrasse 3, D-91058 Erlangen, Germany. ohler@informatik.uni-erlangen.de|University of Erlangen-Nuremberg, Martensstrasse 3, D-91058 Erlangen, Germany. ohler@informatik.uni-erlangen.de|University of Erlangen-Nuremberg, Martensstrasse 3, D-91058 Erlangen, Germany. ohler@informatik.uni-erlangen.de|University of Erlangen-Nuremberg, Martensstrasse 3, D-91058 Erlangen, Germany. ohler@informatik.uni-erlangen.de', 'Germany|Germany|Germany|Germany|Germany', 0, 'Algorithms|Animals|DNA|Drosophila melanogaster|Electronic Data Processing|Eukaryotic Cells|Humans|Markov Chains|Promoter Regions, Genetic', 'Journal Article', '10.1093/bioinformatics/15.5.362', '10366656', 'We describe a new content-based approach for the detection of promoter regions of eukaryotic protein encoding genes. Our system is based on three interpolated Markov chains (IMCs) of different order which are trained on coding, non-coding and promoter sequences. It was recently shown that the interpolation of Markov chains leads to stable parameters and improves on the results in microbial gene finding (Salzberg et al., Nucleic Acids Res., 26, 544-548, 1998). Here, we present new methods for an automated estimation of optimal interpolation parameters and show how the IMCs can be applied to detect promoters in contiguous DNA sequences. Our interpolation approach can also be employed to obtain a reliable scoring function for human coding DNA regions, and the trained models can easily be incorporated in the general framework for gene recognition systems.'),
(69600, 1999, 'bio', 'Statistical mechanical simulation of polymeric DNA melting with MELTSIM', 'Blake, R D|Bizzaro, J W|Blake, J D|Day, G R|Delcourt, S G|Knowles, J|Marx, K A|SantaLucia, J', 'Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA.|Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA.|Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA.|Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA.|Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA.|Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA.|Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA.|Department of Biochemistry, Microbiology and Molecular Biology, University of Maine, Orono, ME 04469-5735, USA.', 'United States|United States|United States|United States|United States|United States|United States|United States', 143, 'Base Composition|Computer Simulation|DNA|DNA, Bacterial|DNA, Fungal|Humans|Models, Statistical|Nucleic Acid Denaturation|Software', 'Journal Article', '10.1093/bioinformatics/15.5.370', '10366657', 'MELTSIM is a windows-based statistical mechanical program for simulating melting curves of DNAs of known sequence and genomic dimensions under different conditions of ionic strength with great accuracy. The program is useful for mapping variations of base compositions of sequences, conducting studies of denaturation, establishing appropriate conditions for hybridization and renaturation, determinations of sequence complexity, and sequence divergence.'),
(69601, 1999, 'bio', 'CRAWview: for viewing splicing variation, gene families, and polymorphism in clusters of ESTs and full-length sequences', 'Chou, A|Burke, J', 'Genome Informatics Group, Pangea Systems, 1999 Harrison Street, Suite 1100, Oakland, CA 94612, USA.|Genome Informatics Group, Pangea Systems, 1999 Harrison Street, Suite 1100, Oakland, CA 94612, USA.', 'United States|United States', 24, 'Alternative Splicing|Expressed Sequence Tags|Genetic Variation|Humans|Multigene Family|Polymorphism, Genetic|Software', 'Journal Article', '10.1093/bioinformatics/15.5.376', '10366658', 'DNA sequence clustering has become a valuable method in support of gene discovery and gene expression analysis. Our interest lies in leveraging the sequence diversity within clusters of expressed sequence tags (ESTs) to model gene structure for the study of gene variants that arise from, among other things, alternative mRNA splicing, polymorphism, and divergence after gene duplication, fusion, and translocation events. In previous work, CRAW was developed to discover gene variants from assembled clusters of ESTs. Most importantly, novel gene features (the differing units between gene variants, for example alternative exons, polymorphisms, transposable elements, etc.) that are specialized to tissue, disease, population, or developmental states can be identified when these tools collate DNA source information with gene variant discrimination. While the goal is complete automation of novel feature and gene variant detection, current methods are far from perfect and hence the development of effective tools for visualization and exploratory data analysis are of paramount importance in the process of sifting through candidate genes and validating targets.'),
(69602, 1999, 'bio', 'PIR-ALN: a database of protein sequence alignments', 'Srinivasarao, G Y|Yeh, L S|Marzec, C R|Orcutt, B C|Barker, W C', 'Protein Information Resource (PIR), National Biomedical Research Foundation, 3900 Reservoir Road NW, Washington, DC 20007, USA. Geetha@nbrf.georgetown.edu|Protein Information Resource (PIR), National Biomedical Research Foundation, 3900 Reservoir Road NW, Washington, DC 20007, USA. Geetha@nbrf.georgetown.edu|Protein Information Resource (PIR), National Biomedical Research Foundation, 3900 Reservoir Road NW, Washington, DC 20007, USA. Geetha@nbrf.georgetown.edu|Protein Information Resource (PIR), National Biomedical Research Foundation, 3900 Reservoir Road NW, Washington, DC 20007, USA. Geetha@nbrf.georgetown.edu|Protein Information Resource (PIR), National Biomedical Research Foundation, 3900 Reservoir Road NW, Washington, DC 20007, USA. Geetha@nbrf.georgetown.edu', 'United States|United States|United States|United States|United States', 22, 'Amino Acid Sequence|Databases, Factual|Molecular Sequence Data|Proteins|Sequence Alignment', 'Journal Article', '10.1093/bioinformatics/15.5.382', '10366659', 'The Protein Information Resource (PIR) maintains a database of annotated and curated alignments in order to visually represent interrelationships among sequences in the PIR-International Protein Sequence Database, to spread and standardize protein names, features and keywords among members of a family or superfamily, and to aid us in classifying sequences, in identifying conserved regions, and in defining new homology domains.'),
(69603, 1999, 'bio', 'Automated genome sequence analysis and annotation', 'Andrade, M A|Brown, N P|Leroy, C|Hoersch, S|de Daruvar, A|Reich, C|Franchini, A|Tamames, J|Valencia, A|Ouzounis, C|Sander, C', 'European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.|European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.|European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.|European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.|European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.|European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.|European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.|European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.|European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.|European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.|European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Cambridge CB10 1SD, UK.', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom', 161, 'Amino Acid Sequence|Automation|Computer Systems|Databases, Factual|Humans|Molecular Sequence Data|Proteins|Sequence Analysis|Software', 'Journal Article', '10.1093/bioinformatics/15.5.391', '10366660', 'Large-scale genome projects generate a rapidly increasing number of sequences, most of them biochemically uncharacterized. Research in bioinformatics contributes to the development of methods for the computational characterization of these sequences. However, the installation and application of these methods require experience and are time consuming.'),
(69604, 1999, 'bio', 'Improved performance in protein secondary structure prediction by inhomogeneous score combination', 'Guermeur, Y|Geourjon, C|Gallinari, P|Deléage, G', 'LIP, Ecole Normale Supérieure de Lyon, 46, Allée dItalie, 69364 Lyon cedex 07, France. Yann.Guermeur@ens-lyon.fr|LIP, Ecole Normale Supérieure de Lyon, 46, Allée dItalie, 69364 Lyon cedex 07, France. Yann.Guermeur@ens-lyon.fr|LIP, Ecole Normale Supérieure de Lyon, 46, Allée dItalie, 69364 Lyon cedex 07, France. Yann.Guermeur@ens-lyon.fr|LIP, Ecole Normale Supérieure de Lyon, 46, Allée dItalie, 69364 Lyon cedex 07, France. Yann.Guermeur@ens-lyon.fr', 'France|France|France|France', 168, 'Amino Acid Sequence|Computer Simulation|Databases, Factual|Models, Molecular|Molecular Sequence Data|Neural Networks (Computer)|Pattern Recognition, Automated|Protein Structure, Secondary', 'Journal Article', '10.1093/bioinformatics/15.5.413', '10366661', 'In many fields of pattern recognition, combination has proved efficient to increase the generalization performance of individual prediction methods. Numerous systems have been developed for protein secondary structure prediction, based on different principles. Finding better ensemble methods for this task may thus become crucial. Furthermore, efforts need to be made to help the biologist in the post-processing of the outputs.'),
(69605, 1999, 'bio', 'WebBLAST 20: an integrated solution for organizing and analyzing sequence data', 'Ferlanti, E S|Ryan, J F|Makalowska, I|Baxevanis, A D', 'Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 49, Room 2C-76, Bethesda, MD 20892-4431, USA.|Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 49, Room 2C-76, Bethesda, MD 20892-4431, USA.|Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 49, Room 2C-76, Bethesda, MD 20892-4431, USA.|Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Building 49, Room 2C-76, Bethesda, MD 20892-4431, USA.', 'United States|United States|United States|United States', 12, 'Base Sequence|Databases, Factual|Electronic Data Processing|Molecular Sequence Data|Sequence Analysis|Software', 'Journal Article', '10.1093/bioinformatics/15.5.422', '10366662', 'WebBLAST is a suite of programs intended to assist in organizing sequencing data and to provide first-pass sequence analysis in an automated fashion. Data processing is fully automated, with end-users being presented both graphical and tabular summaries of data that can be viewed using any Web browser.'),
(69606, 1999, 'bio', 'JaDis: computing distances between nucleic acid sequences', 'Gonçalves, I|Robinson, M|Perrière, G|Mouchiroud, D', 'Laboratoire de Biométrie, Génétique et Biologie des Populations, UMR CNRS no. 5558, Université Claude Bernard, Lyon 1, 43, bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France. perriere.goncalves@biomserv.univ-lyon1.fr|Laboratoire de Biométrie, Génétique et Biologie des Populations, UMR CNRS no. 5558, Université Claude Bernard, Lyon 1, 43, bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France. perriere.goncalves@biomserv.univ-lyon1.fr|Laboratoire de Biométrie, Génétique et Biologie des Populations, UMR CNRS no. 5558, Université Claude Bernard, Lyon 1, 43, bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France. perriere.goncalves@biomserv.univ-lyon1.fr|Laboratoire de Biométrie, Génétique et Biologie des Populations, UMR CNRS no. 5558, Université Claude Bernard, Lyon 1, 43, bd. du 11 Novembre 1918, 69622 Villeurbanne Cedex, France. perriere.goncalves@biomserv.univ-lyon1.fr', 'France|France|France|France', 22, 'Base Composition|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/15.5.424', '10366663', 'JaDis is a Java application for computing evolutionary distances between nucleic acid sequences and G+C base frequencies. It allows specific comparison of coding sequences, of non-coding sequences or of a non-coding sequence with coding sequences.'),
(69607, 1999, 'bio', 'REPuter: fast computation of maximal repeats in complete genomes', 'Kurtz, S|Schleiermacher, C', 'Technische Fakultät, Universität Bielefeld, Postfach 10 01 31, D-33501 Bielefeld, Germany. kurtz.icschlei@techfak.uni-bielefeld.de|Technische Fakultät, Universität Bielefeld, Postfach 10 01 31, D-33501 Bielefeld, Germany. kurtz.icschlei@techfak.uni-bielefeld.de', 'Germany|Germany', 274, 'DNA|Genome|Repetitive Sequences, Nucleic Acid|Software', 'Journal Article', '10.1093/bioinformatics/15.5.426', '10366664', 'A software tool was implemented that computes exact repeats and palindromes in entire genomes very efficiently.'),
(69608, 1999, 'bio', 'Class II MHC quantitative binding motifs derived from a large molecular database with a versatile iterative stepwise discriminant analysis meta-algorithm', 'Mallios, R R', 'Medical Information Resources, University of California, San Francisco, 2615 East Clinton Avenue, Fresno, CA 93703, USA. ronna@ucsfresno.edu', 'United States', 33, 'Algorithms|Amino Acid Sequence|Binding Sites|Computational Biology|Databases, Factual|Discriminant Analysis|Epitopes|HLA-DR1 Antigen|Histocompatibility Antigens Class II|Humans|In Vitro Techniques|Models, Biological|Molecular Sequence Data|Peptides|Protein Binding', 'Journal Article', '10.1093/bioinformatics/15.6.432', '10383468', 'The identification of T-cell epitopes can be crucial for vaccine development. An epitope is a peptide segment that binds to both a T-cell receptor and a major histocompatibility complex (MHC) molecule. Predicting which peptide segments bind MHC molecules is the first step in epitope prediction.'),
(69609, 1999, 'bio', 'Fast evaluation of internal loops in RNA secondary structure prediction', 'Lyngsø, R B|Zuker, M|Pedersen, C N', 'Department of Computer Science, University of Aarhus, DK 8000 Arhus, Denmark. rlyngsoe@daimi.au.dk|Department of Computer Science, University of Aarhus, DK 8000 Arhus, Denmark. rlyngsoe@daimi.au.dk|Department of Computer Science, University of Aarhus, DK 8000 Arhus, Denmark. rlyngsoe@daimi.au.dk', 'Denmark|Denmark|Denmark', 118, 'Algorithms|Computational Biology|Internet|Nucleic Acid Conformation|RNA|Software|Thermodynamics', 'Journal Article', '10.1093/bioinformatics/15.6.440', '10383469', 'Though not as abundant in known biological processes as proteins, RNA molecules serve as more than mere intermediaries between DNA and proteins. Research in the last 15 years demonstrates that RNA molecules serve in many roles, including catalysis. Furthermore, RNA secondary structure prediction based on free energy rules for stacking and loop formation remains one of the few major breakthroughs in the field of structure prediction, as minimum free energy structures and related quantities can be computed with full mathematical rigor. However, with the current energy parameters, the algorithms used hitherto suffer the disadvantage of either employing heuristics that risk (though highly unlikely) missing the optimal structure or becoming prohibitively time consuming for moderate to large sequences.'),
(69610, 1999, 'bio', 'RNA secondary structure prediction using stochastic context-free grammars and evolutionary history', 'Knudsen, B|Hein, J', 'Department of Genetics and Ecology, The Institute of Biological Sciences, University of Aarhus, Building 550, Ny Munkegade, 8000 Aarhus C, Denmark. bk@imf.au.dk|Department of Genetics and Ecology, The Institute of Biological Sciences, University of Aarhus, Building 550, Ny Munkegade, 8000 Aarhus C, Denmark. bk@imf.au.dk', 'Denmark|Denmark', 259, 'Algorithms|Base Sequence|Biological Evolution|Computational Biology|Computer Simulation|Endoribonucleases|Molecular Sequence Data|Nucleic Acid Conformation|Probability|RNA|RNA, Bacterial|RNA, Catalytic|Ribonuclease P|Sequence Homology, Nucleic Acid|Stochastic Processes', 'Journal Article', '10.1093/bioinformatics/15.6.446', '10383470', 'Many computerized methods for RNA secondary structure prediction have been developed. Few of these methods, however, employ an evolutionary model, thus relevant information is often left out from the structure determination. This paper introduces a method which incorporates evolutionary history into RNA secondary structure prediction. The method reported here is based on stochastic context-free grammars (SCFGs) to give a prior probability distribution of structures.'),
(69611, 1999, 'bio', 'Family pairwise search with embedded motif models', 'Grundy, W N|Bailey, T L', 'Department of Computer Science, University of California, Santa Cruz, CA 95064 and NPACI/SDSC, MC 0505, 9500 Gilman Drive, Bldg 109, La Jolla, CA 92093-0505, USA. bgrundy@cse.ucsc.edu|Department of Computer Science, University of California, Santa Cruz, CA 95064 and NPACI/SDSC, MC 0505, 9500 Gilman Drive, Bldg 109, La Jolla, CA 92093-0505, USA. bgrundy@cse.ucsc.edu', 'United States|United States', 14, 'Algorithms|Computational Biology|Models, Statistical|Proteins|Sequence Alignment|Sequence Homology, Amino Acid|Software', 'Comparative Study', '10.1093/bioinformatics/15.6.463', '10383471', 'Statistical models of protein families, such as position-specific scoring matrices, profiles and hidden Markov models, have been used effectively to find remote homologs when given a set of known protein family members. Unfortunately, training these models typically requires a relatively large set of training sequences. Recent work (Grundy, J. Comput. Biol., 5,<479-492, 1998) has shown that, when only a few family members are known, several theoretically justified statistical modeling techniques fail to provide homology detection performance on a par with Family Pairwise Search (FPS), an algorithm that combines scores from a pairwise sequence similarity algorithm such as BLAST.'),
(69612, 1999, 'bio', 'Blocks+: a non-redundant database of protein alignment blocks derived from multiple compilations', 'Henikoff, S|Henikoff, J G|Pietrokovski, S', 'Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA. steveh@fhcrc.org|Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA. steveh@fhcrc.org|Howard Hughes Medical Institute, Fred Hutchinson Cancer Research Center, 1100 Fairview Avenue North, Seattle, WA 98109-1024, USA. steveh@fhcrc.org', 'United States|United States|United States', 236, 'Adenosine Triphosphatases|Algorithms|Amino Acid Sequence|Animals|Computational Biology|DNA Helicases|DNA-Binding Proteins|Databases, Factual|Humans|Molecular Sequence Data|Nuclear Proteins|Proteins|Sequence Alignment|Sequence Homology, Amino Acid|Software|Software Design|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/15.6.471', '10383472', 'As databanks grow, sequence classification and prediction of function by searching protein family databases becomes increasingly valuable. The original Blocks Database, which contains ungapped multiple alignments for families documented in Prosite, can be searched to classify new sequences. However, Prosite is incomplete, and families from other databases are now available to expand coverage of the Blocks Database.'),
(69613, 1999, 'bio', 'A comparison of sequence and structure protein domain families as a basis for structural genomics', 'Elofsson, A|Sonnhammer, E L', 'Department of Biochemistry, Stockholm University, 106 91 Stockholm, Sweden. arne@biokemi.su.se|Department of Biochemistry, Stockholm University, 106 91 Stockholm, Sweden. arne@biokemi.su.se', 'Sweden|Sweden', 46, 'Computational Biology|Databases, Factual|Genome|Protein Folding|Proteins|Sequence Alignment|Sequence Homology, Amino Acid', 'Comparative Study', '10.1093/bioinformatics/15.6.480', '10383473', 'Protein families can be defined based on structure or sequence similarity. We wanted to compare two protein family databases, one based on structural and one on sequence similarity, to investigate to what extent they overlap, the similarity in definition of corresponding families, and to create a list of large protein families with unknown structure as a resource for structural genomics. We also wanted to increase the sensitivity of fold assignment by exploiting protein family HMMs.'),
(69614, 1999, 'bio', 'Clustering of non-polar contacts in proteins', 'Drabløs, F', 'SINTEF Unimed MR Centre, N-7465 Trondheim, Norway. finn.drablos@unimed.sintef.no', 'Norway', 16, 'Algorithms|Binding Sites|Cluster Analysis|Computational Biology|Drug Stability|Esterases|Human Growth Hormone|Humans|Lipase|Models, Molecular|Plant Proteins|Protein Conformation|Protein Folding|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/15.6.501', '10383474', 'Hydrophobic or non-polar contacts in proteins are important for protein folding, protein stability and protein-protein interactions. In particular, in the interior of a protein, in the hydrophobic core, a large number of such contacts are found. The residues involved in these contacts often form a tightly packed cluster of atoms. It is useful for the understanding of protein structure to be able to identify and analyse such clusters.'),
(69615, 1999, 'bio', 'An ontology for bioinformatics applications', 'Baker, P G|Goble, C A|Bechhofer, S|Paton, N W|Stevens, R|Brass, A', 'School of Biological Sciences and Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK. tambis@cs.man.ac.uk|School of Biological Sciences and Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK. tambis@cs.man.ac.uk|School of Biological Sciences and Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK. tambis@cs.man.ac.uk|School of Biological Sciences and Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK. tambis@cs.man.ac.uk|School of Biological Sciences and Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK. tambis@cs.man.ac.uk|School of Biological Sciences and Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PT, UK. tambis@cs.man.ac.uk', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom', 141, 'Animals|Classification|Computational Biology|Databases, Factual|Expert Systems|Models, Biological', 'Journal Article', '10.1093/bioinformatics/15.6.510', '10383475', 'An ontology of biological terminology provides a model of biological concepts that can be used to form a semantic framework for many data storage, retrieval and analysis tasks. Such a semantic framework could be used to underpin a range of important bioinformatics tasks, such as the querying of heterogeneous bioinformatics sources or the systematic annotation of experimental results.'),
(69616, 1999, 'bio', 'Protein analyst--a distributed object environment for protein sequence and structure analysis', 'Saqi, M A|Wild, D L|Hartshorn, M J', 'Bioinformatics Group, GlaxoWellcome Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK. mass15599@ggr.co.uk|Bioinformatics Group, GlaxoWellcome Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK. mass15599@ggr.co.uk|Bioinformatics Group, GlaxoWellcome Medicines Research Centre, Gunnels Wood Road, Stevenage SG1 2NY, UK. mass15599@ggr.co.uk', 'United Kingdom|United Kingdom|United Kingdom', 5, 'Algorithms|Computational Biology|Evaluation Studies as Topic|Models, Molecular|Protein Structure, Secondary|Proteins|Sequence Alignment|Sequence Analysis|Sequence Homology, Amino Acid|Software|Software Design', 'Journal Article', '10.1093/bioinformatics/15.6.521', '10383476', 'Protein Analyst is a flexible tool for the analysis of protein sequences with emphasis on the integration of sequence and structural information.'),
(69617, 1999, 'bio', 'BLAST PRINTS--alternative perspectives on sequence similarity', 'Wright, W|Scordis, P|Attwood, T K', 'School of Biological Sciences, Stopford Building, The University of Manchester, Oxford Road, Manchester M13 6PT, UK. wright@biochemistry.ucl.ac.uk|School of Biological Sciences, Stopford Building, The University of Manchester, Oxford Road, Manchester M13 6PT, UK. wright@biochemistry.ucl.ac.uk|School of Biological Sciences, Stopford Building, The University of Manchester, Oxford Road, Manchester M13 6PT, UK. wright@biochemistry.ucl.ac.uk', 'United Kingdom|United Kingdom|United Kingdom', 14, 'Animals|Computational Biology|DNA|Databases, Factual|Evaluation Studies as Topic|Humans|Proteins|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/15.6.523', '10383477', 'An implementation of BLAST for searching the PRINTS database is presented. The interface allows submission of either protein or DNA queries, and returns the familiar form of output, but modified by means of direct links both to the familial discriminators in PRINTS and to fingerprint profile visualization software. The server thus couples the rapidity of BLAST searching with the sensitivity of fingerprint diagnoses, providing alternative perspectives on a given query.'),
(69618, 1999, 'bio', 'SECOST: sequence-conformation-structure database for amino acid residues in proteins', 'Shats, O|Vaisman, I I|Shats, A|Sherman, S', 'Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.|Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.|Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.|Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 986805 Nebraska Medical Center, Omaha, NE 68198-6805, USA.', 'United States|United States|United States|United States', 0, 'Computational Biology|Databases, Factual|Evaluation Studies as Topic|Protein Conformation|Protein Structure, Secondary|Proteins|Sequence Analysis', 'Journal Article', '10.1093/bioinformatics/15.6.525', '10383478', 'The sequence-conformation-structure database for amino acid residues contains information on 114 828 individual residues derived from the spatial structures of 473 high-quality non-homologous proteins. The information in the database is obtained using a variety of different methods and can be used in various protein modeling applications.'),
(69619, 1999, 'bio', 'Local sequence alignments with monotonic gap penalties', 'Mott, R', 'SmithKline-Beecham Pharmaceuticals R & D, New Frontiers Science Park (North),3rd Avenue, Harlow CM19 5AW, UK. Richard.Mott@well.ox.ac.uk', 'United Kingdom', 23, 'Algorithms|Computational Biology|Evaluation Studies as Topic|Sensitivity and Specificity|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/15.6.455', '10383814', 'Sequence alignments obtained using affine gap penalties are not always biologically correct, because the insertion of long gaps is over-penalised. There is a need for an efficient algorithm which can find local alignments using non-linear gap penalties.'),
(69620, 1999, 'bio', 'The emerging paradigm and open problems in comparative genomics', 'Koonin, E V', 'SmithKline-Beecham Pharmaceuticals R & D, New Frontiers Science Park (North),3rd Avenue, Harlow CM19 5AW, UK. Richard.Mott@well.ox.ac.uk', 'United Kingdom', 30, 'Genome', 'Editorial', '10.1093/bioinformatics/15.4.265', '10438229', '-'),
(69621, 1999, 'bio', 'The new biological literature', 'Gribskov, M', 'SmithKline-Beecham Pharmaceuticals R & D, New Frontiers Science Park (North),3rd Avenue, Harlow CM19 5AW, UK. Richard.Mott@well.ox.ac.uk', 'United Kingdom', 0, 'Biology|Computational Biology|Databases, Factual', 'Editorial', '10.1093/bioinformatics/15.5.347', '10484667', '-'),
(69622, 1999, 'bio', 'Evaluation of human-readable annotation in biomolecular sequence databases with biological rule libraries', 'Eisenhaber, F|Bork, P', 'Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13122 Berlin-Buch, Germany. Frank.Eisenhaber@embl-heidelberg.de|Max-Delbrück-Centrum für Molekulare Medizin, Robert-Rössle-Strasse 10, 13122 Berlin-Buch, Germany. Frank.Eisenhaber@embl-heidelberg.de', 'Germany|Germany', 39, 'Algorithms|Animals|Databases, Factual|Genomic Library|Humans|Molecular Sequence Data|Protein Structure, Tertiary|Proteins|Software|Subcellular Fractions', 'Journal Article', '10.1093/bioinformatics/15.7.528', '10487860', 'Computer-based selection of entries from sequence databases with respect to a related functional description, e.g. with respect to a common cellular localization or contributing to the same phenotypic function, is a difficult task. Automatic semantic analysis of annotations is not only hampered by incomplete functional assignments. A major problem is that annotations are written in a rich, non-formalized language and are meant for reading by a human expert. This person can extract from the text considerably more information than is immediately apparent due to his extended biological background knowledge and logical reasoning.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(69623, 1999, 'bio', 'Complete genomes in WWW Entrez: data representation and analysis', 'Tatusova, T A|Karsch-Mizrachi, I|Ostell, J A', 'National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, MD 208944, USA. tatiana@ncbi.nlm.nih.gov|National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, MD 208944, USA. tatiana@ncbi.nlm.nih.gov|National Center for Biotechnology Information (NCBI), National Library of Medicine, National Institutes of Health, Bethesda, MD 208944, USA. tatiana@ncbi.nlm.nih.gov', 'United States|United States|United States', 89, 'Amino Acid Sequence|Chromosomes|Databases, Factual|Genome|Genome, Archaeal|Genome, Bacterial|Genome, Fungal|Genome, Viral|Internet|Molecular Sequence Data|National Library of Medicine (U.S.)|Open Reading Frames|Proteins|Sequence Alignment|United States', 'Journal Article', '10.1093/bioinformatics/15.7.536', '10487861', 'The large amount of genome sequence data now publicly available can be accessed through the National Center for Biotechnology Information (NCBI) Entrez search and retrieval system, making it possible to explore data of a breadth and scope exceeding traditional flatfile views.'),
(69624, 1999, 'bio', 'Development of the receptor database (RDB): application to the endocrine disruptor problem', 'Nakata, K|Takai, T|Kaminuma, T', 'Division of Chem-Bio Informatics, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan. nakata@nihs.go.jp|Division of Chem-Bio Informatics, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan. nakata@nihs.go.jp|Division of Chem-Bio Informatics, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya-ku, Tokyo 158-8501, Japan. nakata@nihs.go.jp', 'Japan|Japan|Japan', 11, 'Amino Acid Sequence|Animals|Computer Systems|Database Management Systems|Databases, Factual|Humans|Internet|Models, Molecular|Molecular Sequence Data|Protein Conformation|Protein Structure, Secondary|Receptors, Cell Surface|Sequence Alignment|Sequence Homology, Amino Acid', 'Journal Article', '10.1093/bioinformatics/15.7.544', '10487862', 'To represent various aspects of receptors effectively, we developed the receptor database (RDB), using an object-oriented database management system ACEDB and the Internet/WWW technology.'),
(69625, 1999, 'bio', 'Regression trees for analysis of mutational spectra in nucleotide sequences', 'Berikov, V B|Rogozin, I B', 'Institute of Mathematics and Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. berikov@math.nsc.ru|Institute of Mathematics and Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia. berikov@math.nsc.ru', '-|-', 11, 'Algorithms|Alkylating Agents|Base Sequence|DNA Mutational Analysis|Escherichia coli|Ethylnitrosourea|Lac Operon|Models, Genetic|Models, Theoretical|Mutation|Regression Analysis|Software', 'Journal Article', '10.1093/bioinformatics/15.7.553', '10487863', 'The study and comparison of mutational spectra is an important problem in molecular biology, because these spectra often reveal important features of the action of various mutagens and the functioning of repair/replication enzymes. As is known, mutability varies significantly along nucleotide sequences: mutations often concentrate at certain positions in a sequence, otherwise termed hotspots.'),
(69626, 1999, 'bio', 'Identifying DNA and protein patterns with statistically significant alignments of multiple sequences', 'Hertz, G Z|Stormo, G D', 'Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA. hertz@colorado.edu|Department of Molecular, Cellular and Developmental Biology, University of Colorado, Boulder, CO 80309-0347, USA. hertz@colorado.edu', 'United States|United States', 894, 'Algorithms|Bacterial Proteins|Base Sequence|Binding Sites|Carrier Proteins|Cyclic AMP Receptor Protein|DNA|DNA, Bacterial|Escherichia coli|Linear Models|Proteins|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/15.7.563', '10487864', 'Molecular biologists frequently can obtain interesting insight by aligning a set of related DNA, RNA or protein sequences. Such alignments can be used to determine either evolutionary or functional relationships. Our interest is in identifying functional relationships. Unless the sequences are very similar, it is necessary to have a specific strategy for measuring-or scoring-the relatedness of the aligned sequences. If the alignment is not known, one can be determined by finding an alignment that optimizes the scoring scheme.'),
(69627, 1999, 'bio', 'Analysis of base-pairing potentials between 16S rRNA and 5 UTR for translation initiation in various prokaryotes', 'Osada, Y|Saito, R|Tomita, M', 'Laboratory for Bioinformatics, Keio University, 5322 Endo, Fujisawa, 252, Japan.|Laboratory for Bioinformatics, Keio University, 5322 Endo, Fujisawa, 252, Japan.|Laboratory for Bioinformatics, Keio University, 5322 Endo, Fujisawa, 252, Japan.', 'Japan|Japan|Japan', 63, '5 Untranslated Regions|Archaea|Bacteria|Base Pairing|Base Sequence|Codon, Initiator|Escherichia coli|Genome|Peptide Chain Initiation, Translational|Prokaryotic Cells|RNA, Bacterial|RNA, Ribosomal, 16S|Saccharomyces cerevisiae|Thermodynamics', 'Comparative Study', '10.1093/bioinformatics/15.7.578', '10487865', 'It is well accepted that the 3 end of 16S rRNA is directly involved in prokaryotic translation initiation by pairing with the Shine-Dalgarno (SD) sequence, which is located in the ribosome-binding site of mRNA. According to Shine and Dalgarno, Escherichia coli s 5 UTR has the pattern of AGGAGG (SD sequence), which is complementary to the 3 end sequence of 16S rRNA. In this work, we systematically calculated free-energy values of the base pairing between the 3 end of 16S rRNA and the 5 UTR of mRNA, in order to analyze the base-pairing potentials in various prokaryotes. The free-energy values were then plotted over distances from the start codon to visualize the free-energy pattern of 5UTRs.'),
(69628, 1999, 'bio', 'Nucleosomal DNA property database', 'Levitsky, V G|Ponomarenko, M P|Ponomarenko, J V|Frolov, A S|Kolchanov, N A', 'Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 630090, Lavrentieva 10, Novosibirsk, Russia. levitsky@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 630090, Lavrentieva 10, Novosibirsk, Russia. levitsky@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 630090, Lavrentieva 10, Novosibirsk, Russia. levitsky@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 630090, Lavrentieva 10, Novosibirsk, Russia. levitsky@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 630090, Lavrentieva 10, Novosibirsk, Russia. levitsky@bionet.nsc.ru', '-|-|-|-|-', 23, 'Algorithms|Animals|Binding Sites|Chemical Phenomena|Chemistry, Physical|DNA|Databases, Factual|Humans|Nucleosomes|Software', 'Journal Article', '10.1093/bioinformatics/15.7.582', '10487866', 'Chromatin structure plays the crucial role in proper gene functioning. Therefore, it is very important to investigate nucleosomal DNA properties and recognize genome nucleosome positioning sequences. Nevertheless, applying different sequence analysis methods separately is insufficient for complete nucleosomal DNA description. One of the most probable reasons for that is the weakness of nucleosome positioning signals. The present paper offers a set of methods to reveal the most important nucleosomal DNA characteristics and to show a common pattern of nucleosome site properties.'),
(69629, 1999, 'bio', 'Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis', 'Mendoza, L|Thieffry, D|Alvarez-Buylla, E R', 'Instituto de Ecología, UNAM, Ap. Postal 70-275, Coyoacán, DF, CP04510, Mexico. lams@servidor.unam.mx|Instituto de Ecología, UNAM, Ap. Postal 70-275, Coyoacán, DF, CP04510, Mexico. lams@servidor.unam.mx|Instituto de Ecología, UNAM, Ap. Postal 70-275, Coyoacán, DF, CP04510, Mexico. lams@servidor.unam.mx', 'Mexico|Mexico|Mexico', 208, 'Arabidopsis|Feedback|Gene Expression Regulation, Developmental|Gene Expression Regulation, Plant|Genes, Plant|Logistic Models|Models, Genetic|Mutation|Phenotype', 'Journal Article', '10.1093/bioinformatics/15.7.593', '10487867', 'A large number of molecular mechanisms at the basis of gene regulation have been described during the last few decades. It is now becoming possible to address questions dealing with both the structure and the dynamics of genetic regulatory networks, at least in the case of some of the best-characterized organisms. Most recent attempts to address these questions deal with microbial or animal model systems. In contrast, we analyze here a gene network involved in the control of the morphogenesis of flowers in a model plant, Arabidopsis thaliana.'),
(69630, 1999, 'bio', 'SCPD: a promoter database of the yeast Saccharomyces cerevisiae', 'Zhu, J|Zhang, M Q', 'Cold Spring Harbor Laboratory, PO Box 100, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. zhuj@cshl.org|Cold Spring Harbor Laboratory, PO Box 100, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA. zhuj@cshl.org', 'United States|United States', 333, 'Binding Sites|Databases, Factual|Genes, Fungal|Genes, Regulator|Genome, Fungal|Promoter Regions, Genetic|Saccharomyces cerevisiae|TATA Box|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/15.7.607', '10487868', 'In order to facilitate a systematic study of the promoters and transcriptionally regulatory cis-elements of the yeast Saccharomyces cerevisiae on a genomic scale, we have developed a comprehensive yeast-specific promoter database, SCPD.'),
(69631, 1999, 'bio', 'GeneBuilder: interactive in silico prediction of gene structure', 'Milanesi, L|DAngelo, D|Rogozin, I B', 'Istituto di Tecnologie Biomediche Avanzate CNR, via Fratelli Cervi 93, 20090 Segrate, Milano, Italy. milanesi@itba.mi.cnr.it|Istituto di Tecnologie Biomediche Avanzate CNR, via Fratelli Cervi 93, 20090 Segrate, Milano, Italy. milanesi@itba.mi.cnr.it|Istituto di Tecnologie Biomediche Avanzate CNR, via Fratelli Cervi 93, 20090 Segrate, Milano, Italy. milanesi@itba.mi.cnr.it', 'Italy|Italy|Italy', 47, 'Amino Acid Sequence|Animals|Base Sequence|Binding Sites|Codon|CpG Islands|DNA|Databases, Factual|Expressed Sequence Tags|Genes|Humans|Internet|Molecular Sequence Data|Sequence Alignment|Software|TATA Box|Transcription Factors|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/15.7.612', '10487869', 'Prediction of gene structure in newly sequenced DNA becomes very important in large genome sequencing projects. This problem is complicated due to the exon-intron structure of eukaryotic genes and because gene expression is regulated by many different short nucleotide domains. In order to be able to analyse the full gene structure in different organisms, it is necessary to combine information about potential functional signals (promoter region, splice sites, start and stop codons, 3 untranslated region) together with the statistical properties of coding sequences (coding potential), information about homologous proteins, ESTs and repeated elements.'),
(69632, 1999, 'bio', 'Estimating transcription factor bindability on DNA', 'Tsunoda, T|Takagi, T', 'Genome Data Base, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. tatsu@ims.u-tokyo.ac.jp|Genome Data Base, Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. tatsu@ims.u-tokyo.ac.jp', 'Japan|Japan', 197, 'Algorithms|Animals|Binding Sites|DNA|Databases, Factual|Promoter Regions, Genetic|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/15.7.622', '10487870', 'Precise analysis of the genetic network, gene function and transcription regulation requires accurate prediction of transcription factor (TF) bindability on DNA. For calculating the matching score between an input sequence and a set of known TF binding sites, we use positional weight matrices (PWMs) and Buchers calculating method (Bucher, J. Mol. Biol., 212, 563-578, 1990). Since estimating TF binding sites requires cut-off values, we propose a robust cut-off value determining algorithm.'),
(69633, 1999, 'bio', 'Oligonucleotide frequency matrices addressed to recognizing functional DNA sites', 'Ponomarenko, M P|Ponomarenko, J V|Frolov, A S|Podkolodnaya, O A|Vorobyev, D G|Kolchanov, N A|Overton, G C', 'Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyeva Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyeva Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyeva Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyeva Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyeva Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyeva Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyeva Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru', '-|-|-|-|-|-|-', 30, 'Algorithms|Base Sequence|Binding Sites|DNA|DNA-Binding Proteins|Databases, Factual|Genome|Molecular Sequence Data|NFI Transcription Factors|Oligodeoxyribonucleotides|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/15.7.631', '10487871', 'Recognition of functional sites remains a key event in the course of genomic DNA annotation. It is well known that a number of sites have their own specific oligonucleotide content. This pinpoints the fact that the preference of the site-specific nucleotide combinations at adjacent positions within an analyzed functional site could be informative for this site recognition. Hence, Web-available resources describing the site-specific oligonucleotide content of the functional DNA sites and applying the above approach for site recognition are needed. However, they have been poorly developed up to now.'),
(69634, 1999, 'bio', 'Investigating extended regulatory regions of genomic DNA sequences', 'Babenko, V N|Kosarev, P S|Vishnevsky, O V|Levitsky, V G|Basin, V V|Frolov, A S', 'Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Lavrentyev Avenue, 10, Novosibirsk, 630090, Russia. bob@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Lavrentyev Avenue, 10, Novosibirsk, 630090, Russia. bob@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Lavrentyev Avenue, 10, Novosibirsk, 630090, Russia. bob@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Lavrentyev Avenue, 10, Novosibirsk, 630090, Russia. bob@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Lavrentyev Avenue, 10, Novosibirsk, 630090, Russia. bob@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology and Genetics, Lavrentyev Avenue, 10, Novosibirsk, 630090, Russia. bob@bionet.nsc.ru', '-|-|-|-|-|-', 29, 'Algorithms|Animals|Base Sequence|Computer Systems|CpG Islands|DNA|Databases, Factual|Genes, Regulator|Internet|Promoter Regions, Genetic|Software|TATA Box', 'Journal Article', '10.1093/bioinformatics/15.7.644', '10487872', 'Despite the growing volume of data on primary nucleotide sequences, the regulatory regions remain a major puzzle with regard to their function. Numerous recognising programs considering a diversity of properties of regulatory regions have been developed. The system proposed here allows the specific contextual, conformational and physico-chemical properties to be revealed based on analysis of extended DNA regions.'),
(69635, 1999, 'bio', 'Conformational and physicochemical DNA features specific for transcription factor binding sites', 'Ponomarenko, J V|Ponomarenko, M P|Frolov, A S|Vorobyev, D G|Overton, G C|Kolchanov, N A', 'Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru', '-|-|-|-|-|-', 58, 'Base Sequence|Binding Sites|Chemical Phenomena|Chemistry, Physical|DNA|Databases, Factual|Internet|Molecular Sequence Data|Nucleic Acid Conformation|Software|TATA Box|Transcription Factors', 'Comparative Study', '10.1093/bioinformatics/15.7.654', '10487873', 'A reliable recognition of transcription factor binding sites is essential for analysis of regulatory genomic sequences. The experimental data make evident an important role of DNA conformational features for site functioning. However, Internet-available tools for revealing conformational and physicochemical DNA features significant for the site functioning and subsequent use of these features for site recognition have not been developed up to now.'),
(69636, 1999, 'bio', 'Integrated databases and computer systems for studying eukaryotic gene expression', 'Kolchanov, N A|Ponomarenko, M P|Frolov, A S|Ananko, E A|Kolpakov, F A|Ignatieva, E V|Podkolodnaya, O A|Goryachkovskaya, T N|Stepanenko, I L|Merkulova, T I|Babenko, V V|Ponomarenko, Y V|Kochetov, A V|Podkolodny, N L|Vorobiev, D V|Lavryushev, S V|Grigorovich, D A|Kondrakhin, Y V|Milanesi, L|Wingender, E|Solovyev, V|Overton, G C', 'Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru|Institute of Cytology & Genetics, Siberian Branch of the Russian Academy of Sciences, Prosp. Lavrentieva 10, Novosibirsk 630090, Russia. kol@bionet.nsc.ru', '-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-|-', 18, 'Algorithms|Artificial Intelligence|Base Sequence|Binding Sites|Chemical Phenomena|Chemistry, Physical|Computer Systems|DNA|Databases, Factual|Eukaryotic Cells|Gene Expression|Internet|Nucleic Acid Conformation|Promoter Regions, Genetic|Protein Biosynthesis|RNA, Messenger|Software|TATA Box|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/15.7.669', '10487874', 'The goal of the work was to develop a WWW-oriented computer system providing a maximal integration of informational and software resources on the regulation of gene expression and navigation through them. Rapid growth of the variety and volume of information accumulated in the databases on regulation of gene expression necessarily requires the development of computer systems for automated discovery of the knowledge that can be further used for analysis of regulatory genomic sequences.'),
(69637, 1999, 'bio', 'Identification of sequence-dependent DNA features correlating to activity of DNA sites interacting with proteins', 'Ponomarenko, M P|Ponomarenko, J V|Frolov, A S|Podkolodny, N L|Savinkova, L K|Kolchanov, N A|Overton, G C', 'Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. pon@bionet.nsc.ru', '-|-|-|-|-|-|-', 0, 'Algorithms|Animals|Base Sequence|Binding Sites|Chemical Phenomena|Chemistry, Physical|Computer Systems|DNA|Databases, Factual|Humans|MADS Domain Proteins|MEF2 Transcription Factors|Molecular Sequence Data|Mutation|Myogenic Regulatory Factors|Nucleic Acid Conformation|Proteins|TATA Box', 'Journal Article', '10.1093/bioinformatics/15.7.687', '10487875', 'The commonly accepted statistical mechanical theory is now multiply confirmed by using the weight matrix methods successfully recognizing DNA sites binding regulatory proteins in prokaryotes. Nevertheless, the recent evaluation of weight matrix methods application for transcription factor binding site recognition in eukaryotes has unexpectedly revealed that the matrix scores correlate better to each other than to the activity of DNA sites interacting with proteins. This observation points out that molecular mechanisms of DNA/protein recognition are more complicated in eukaryotes than in prokaryotes. As the extra events in eukaryotes, the following processes may be considered: (i) competition between the proteins and nucleosome core particle for DNA sites binding these proteins and (ii) interaction between two synergetic/antagonist proteins recognizing a composed element compiled from two DNA sites binding these proteins. That is why identification of the sequence-dependent DNA features correlating with affinity magnitudes of DNA sites interacting with a protein can pinpoint the molecular event limiting this protein/DNA recognition machinery.'),
(69638, 1999, 'bio', 'Prediction of eukaryotic mRNA translational properties', 'Kochetov, A V|Ponomarenko, M P|Frolov, A S|Kisselev, L L|Kolchanov, N A', 'Institute of Cytology and Genetics, Pr. Lavrentieva 10, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, Moscow, 117984, Russia. AK@bionet.nsc.ru|Institute of Cytology and Genetics, Pr. Lavrentieva 10, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, Moscow, 117984, Russia. AK@bionet.nsc.ru|Institute of Cytology and Genetics, Pr. Lavrentieva 10, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, Moscow, 117984, Russia. AK@bionet.nsc.ru|Institute of Cytology and Genetics, Pr. Lavrentieva 10, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, Moscow, 117984, Russia. AK@bionet.nsc.ru|Institute of Cytology and Genetics, Pr. Lavrentieva 10, Novosibirsk, 630090 and Engelhardt Institute of Molecular Biology, Moscow, 117984, Russia. AK@bionet.nsc.ru', '-|-|-|-|-', 22, '5 Untranslated Regions|Algorithms|Animals|Databases, Factual|Eukaryotic Cells|Gene Expression|Mammals|Nucleic Acid Conformation|Plants|Protein Biosynthesis|RNA, Messenger|Software', 'Journal Article', '10.1093/bioinformatics/15.7.704', '10487876', 'It is well known that eukaryotic mRNAs are translated at different levels depending on their sequence characteristics. Evaluation of mRNA translatability is of importance in prediction of the gene expression pattern by computer methods and to improve the recognition of mRNAs within cloned nucleotide sequences. It may also be used in biotechnological experiments to optimize the expression of foreign genes in transgenic organisms.'),
(69639, 1999, 'bio', 'Interactive data input into the GeneNet database', 'Kolpakov, F A|Ananko, E A', 'Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, Siberian Branch of Russian Academy of Sciences, 633090, Lavrentieva 10, Novosibirsk, Russia. genenet@bionet.nsc.ru|Laboratory of Theoretical Genetics, Institute of Cytology & Genetics, Siberian Branch of Russian Academy of Sciences, 633090, Lavrentieva 10, Novosibirsk, Russia. genenet@bionet.nsc.ru', '-|-', 8, 'Computer Graphics|Computer Systems|Databases, Factual|Genes|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/15.7.713', '10487877', 'The GeneNet database has been developed for a formalized hierarchical description of the gene networks. To provide rapid data accumulation in the database, the Java graphical interface for data input through the Internet by independent experts equipped with convenient visual tools is developed.'),
(69640, 1999, 'bio', 'Financing a future for public biological data', 'Ellis, L B|Kalumbi, D', 'Department of Laboratory Medicine and Pathology and Department of Applied Economics, University of Minnesota, Minneapolis, MN 55455, USA.|Department of Laboratory Medicine and Pathology and Department of Applied Economics, University of Minnesota, Minneapolis, MN 55455, USA.', 'United States|United States', 10, 'Computational Biology|Databases, Factual|Financial Support|Internet|Models, Economic', 'Journal Article', '10.1093/bioinformatics/15.9.717', '10498771', 'The public web-based biological database infrastructure is a source of both wonder and worry. Users delight in the ever increasing amounts of information available, database administrators and curators worry about long-term financial support. An earlier study of 153 biological databases (Ellis and Kalumbi, Nature Biotechnol., 16, 1323-1324, 1998) determined that near future (1-5 year) funding for over two-thirds of them was uncertain. More detailed data are required to determine the magnitude of the problem and offer possible solutions.'),
(69641, 1999, 'bio', 'Neural network input representations that produce accurate consensus sequences from DNA fragment assemblies', 'Allex, C F|Shavlik, J W|Blattner, F R', 'Computer Sciences Department, University of Wisconsin - Madison, 1210 West Dayton Street, Madison, WI 53706, DNASTAR Inc., 1228 South Park Street, Madison, WI 53715, USA.|Computer Sciences Department, University of Wisconsin - Madison, 1210 West Dayton Street, Madison, WI 53706, DNASTAR Inc., 1228 South Park Street, Madison, WI 53715, USA.|Computer Sciences Department, University of Wisconsin - Madison, 1210 West Dayton Street, Madison, WI 53706, DNASTAR Inc., 1228 South Park Street, Madison, WI 53715, USA.', 'United States|United States|United States', 13, 'Base Sequence|Consensus Sequence|DNA Fragmentation|DNA, Bacterial|Escherichia coli|Molecular Sequence Data|Neural Networks (Computer)|Sequence Analysis, DNA', 'Journal Article', '10.1093/bioinformatics/15.9.723', '10498772', 'Given inputs extracted from an aligned column of DNA bases and the underlying Perkin Elmer Applied Biosystems (ABI) fluorescent traces, our goal is to train a neural network to determine correctly the consensus base for the column. Choosing an appropriate network input representation is critical to success in this task. We empirically compare five representations, one uses only base calls and the others include trace information.'),
(69642, 1999, 'bio', 'Shotgun: getting more from sequence similarity searches', 'Pegg, S C|Babbitt, P C', 'Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.|Departments of Biopharmaceutical Sciences and Pharmaceutical Chemistry, University of California, San Francisco, CA 94143, USA.', 'United States|United States', 31, 'Algorithms|Database Management Systems|Databases, Factual|Enoyl-CoA Hydratase|Information Storage and Retrieval|Phosphopyruvate Hydratase|Sequence Analysis|Software', 'Journal Article', '10.1093/bioinformatics/15.9.729', '10498773', 'As genomic sequencing reveals the range of structural classes generated through the evolution of proteins, analysis of the superfamilies to which they belong can contribute important insights for understanding their structure-function relationships. Current database search techniques fall short of identifying the majority of distant sequence relationships at statistically significant levels. We developed the Shotgun program in an effort to enhance the sensitivity and utility of current database search output.'),
(69643, 1999, 'bio', 'Associative database of protein sequences', 'Hanke, J|Lehmann, G|Bork, P|Reich, J G', 'Max-Delbrück-Center for Molecular Medicine, Department of Bioinformatics, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany.|Max-Delbrück-Center for Molecular Medicine, Department of Bioinformatics, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany.|Max-Delbrück-Center for Molecular Medicine, Department of Bioinformatics, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany.|Max-Delbrück-Center for Molecular Medicine, Department of Bioinformatics, Robert-Rössle-Strasse 10, D-13125 Berlin-Buch, Germany.', 'Germany|Germany|Germany|Germany', 2, 'Amino Acid Sequence|Animals|Conserved Sequence|Databases, Factual|Humans|Information Storage and Retrieval|Molecular Sequence Data|Neural Networks (Computer)|Proteins|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/15.9.741', '10498774', 'We present a new concept that combines data storage and data analysis in genome research, based on an associative network memory. As an illustration, 115 000 conserved regions from over 73 000 published sequences (i.e. from the entire annotated part of the SWISSPROT sequence database) were identified and clustered by a self-organizing network. Similarity and kinship, as well as degree of distance between the conserved protein segments, are visualized as neighborhood relationship on a two-dimensional topographical map.'),
(69644, 1999, 'bio', 'Mathematical simulation and analysis of cellular metabolism and regulation', 'Goryanin, I|Hodgman, T C|Selkov, E', 'Laboratory for Metabolic Modeling and Bioinformatics, The Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia, Advanced Technology and Informatics Unit, GlaxoWellcome Medicines Research Centre, Gunnels Wood Road, Stevenage,UK.|Laboratory for Metabolic Modeling and Bioinformatics, The Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia, Advanced Technology and Informatics Unit, GlaxoWellcome Medicines Research Centre, Gunnels Wood Road, Stevenage,UK.|Laboratory for Metabolic Modeling and Bioinformatics, The Russian Academy of Sciences, 142292 Pushchino, Moscow Region, Russia, Advanced Technology and Informatics Unit, GlaxoWellcome Medicines Research Centre, Gunnels Wood Road, Stevenage,UK.', 'United Kingdom|United Kingdom|United Kingdom', 115, 'Algorithms|Cell Physiological Phenomena|Cells|Computer Simulation|Mathematical Computing|Models, Biological', 'Journal Article', '10.1093/bioinformatics/15.9.749', '10498775', 'A better understanding of the biological phenomena observed in cells requires the creation and analysis of mathematical models of cellular metabolism and physiology. The formulation and study of such models must also be simplified as far as possible to cope with the increasing complexity demanded and exponential accumulation of the metabolic reconstructions computed from sequenced genomes.'),
(69645, 1999, 'bio', 'Finding families for genomic ORFans', 'Fischer, D|Eisenberg, D', 'Faculty of Natural Science, Department of Math and Computer Science, Ben Gurion University, Beer-Sheva 84015, Israel. dfischer@cs.bgu.ac.il|Faculty of Natural Science, Department of Math and Computer Science, Ben Gurion University, Beer-Sheva 84015, Israel. dfischer@cs.bgu.ac.il', 'Israel|Israel', 166, 'Bacterial Proteins|Computational Biology|Genes, Bacterial|Open Reading Frames|Proteins', 'Journal Article', '10.1093/bioinformatics/15.9.759', '10498776', '-'),
(69646, 1999, 'bio', 'K-Estimator: calculation of the number of nucleotide substitutions per site and the confidence intervals', 'Comeron, J M', 'Department of Ecology and Evolution, University of Chicago, 1101 East 57th Street, Chicago, IL 60637, USA.', 'United States', 187, 'Base Sequence|Confidence Intervals|DNA Mutational Analysis|Proteins|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/15.9.763', '10498777', 'K-Estimator 4.5 is a Windows program that estimates the number of nucleotide substitutions per site (divergence) when comparing two aligned nucleotide sequences, both protein-coding and non-coding. Confidence intervals of the divergence estimates are obtained by Monte Carlo simulation.'),
(69647, 1999, 'bio', 'TargetDB: a database of peptides targeting proteins to subcellular locations', 'Wei, T|OConnell, M', 'Research Computing Center, Harvard Medical School, 220 Longwood Avenue, Goldenson 259, Boston, MA 02115, USA.|Research Computing Center, Harvard Medical School, 220 Longwood Avenue, Goldenson 259, Boston, MA 02115, USA.', 'United States|United States', 1, 'Biological Transport|Databases, Factual|Eukaryotic Cells|Peptides|Prokaryotic Cells|Proteins', 'Journal Article', '10.1093/bioinformatics/15.9.765', '10498778', 'TargetDB is a relational database designed to represent data on protein targeting sequences, mutant signals, subcellular targets and source organisms.'),
(69648, 1999, 'bio', 'SWEET - WWW-based rapid 3D construction of oligo- and polysaccharides', 'Bohne, A|Lang, E|von der Lieth, C W', 'Deutsches Krebsforschungszentrum, Zentrale Spektroskopie, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.|Deutsches Krebsforschungszentrum, Zentrale Spektroskopie, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.|Deutsches Krebsforschungszentrum, Zentrale Spektroskopie, Im Neuenheimer Feld 280, D-69120 Heidelberg, Germany.', 'Germany|Germany|Germany', 116, 'Carbohydrate Conformation|Carbohydrate Sequence|Internet|Oligosaccharides|Polysaccharides|Software', 'Journal Article', '10.1093/bioinformatics/15.9.767', '10498779', 'SWEET is a WWW-based tool which rapidly converts the commonly used carbohydrate sequence information directly into a preliminary but reliable 3D model which can be visualised and written to files in several ways.'),
(69649, 1999, 'bio', 'MatrixPlot: visualizing sequence constraints', 'Gorodkin, J|Staerfeldt, H H|Lund, O|Brunak, S', 'Center for Biological Sequence Analysis, Department of Biotechnology, The Technical University of Denmark, Lyngby, Denmark.|Center for Biological Sequence Analysis, Department of Biotechnology, The Technical University of Denmark, Lyngby, Denmark.|Center for Biological Sequence Analysis, Department of Biotechnology, The Technical University of Denmark, Lyngby, Denmark.|Center for Biological Sequence Analysis, Department of Biotechnology, The Technical University of Denmark, Lyngby, Denmark.', 'Denmark|Denmark|Denmark|Denmark', 29, 'Nucleic Acids|Proteins|Sequence Alignment|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/15.9.769', '10498780', 'MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot.'),
(69650, 1999, 'bio', 'Swissknife - lazy parsing of SWISS-PROT entries', 'Hermjakob, H|Fleischmann, W|Apweiler, R', 'EMBL Outstation Hinxton, The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.|EMBL Outstation Hinxton, The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.|EMBL Outstation Hinxton, The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.', 'United Kingdom|United Kingdom|United Kingdom', 19, 'Databases, Factual|Proteins|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/15.9.771', '10498781', 'We present Swissknife, a set of Perl modules which provides a fast and reliable object-oriented interface to parsing and modifying files in SWISS-PROT format.'),
(69651, 1999, 'bio', 'Genomes OnLine Database (GOLD 10): a monitor of complete and ongoing genome projects world-wide', 'Kyrpides, N C', 'Department of Microbiology, University of Illinois at Urbana-Champaign, B103 Chemistry and Life Sciences, MC 110, 407 S Goodwin, Urbana, IL 61801, USA.', 'United States', 55, 'Databases, Factual|Genome|Internet', 'Journal Article', '10.1093/bioinformatics/15.9.773', '10498782', 'GOLD (Genomes On Line Database) is a World Wide Web resource for comprehensive access to information regarding complete and ongoing genome projects around the world.'),
(69652, 1999, 'bio', 'E-publishing on the Web: promises, pitfalls, and payoffs for bioinformatics', 'Gerstein, M', 'Department of Microbiology, University of Illinois at Urbana-Champaign, B103 Chemistry and Life Sciences, MC 110, 407 S Goodwin, Urbana, IL 61801, USA.', 'United States', 4, 'Computational Biology|Internet|Publishing', 'Editorial', '10.1093/bioinformatics/15.6.429', '10515701', '-'),
(69653, 1999, 'bio', 'Special issue containing a selection of papers presented at the 1st International Conference on Bioinformatics of Genome Regulation and Structure BGRS 98 Novosibirsk, Altai Mountains, Russia 24-31 August 1998', '-', '-', '-', 4, 'Animals|Computational Biology|Genome|Humans', 'Congress', '10.1093/bioinformatics/15.6.429', '10627151', '-'),
(69654, 1999, 'bio', 'The Seventh International Conference on Intelligent Systems for Molecular Biology (ISMB99)', 'Lengauer, T', 'Department of Microbiology, University of Illinois at Urbana-Champaign, B103 Chemistry and Life Sciences, MC 110, 407 S Goodwin, Urbana, IL 61801, USA.', 'United States', 0, 'Computational Biology|Molecular Biology|Societies, Scientific', 'Congress', '10.1093/bioinformatics/15.10.775', '10705430', '-'),
(69655, 1999, 'bio', 'Genes regulated cooperatively by one or more transcription factors and their identification in whole eukaryotic genomes', 'Wagner, A', 'Department of Biology, University of New Mexico, Albuquerque, USA. wagnera@unm.edu', 'Mexico', 114, 'Base Sequence|Binding Sites|Computational Biology|DNA, Fungal|Eukaryotic Cells|Gene Expression Regulation|Genome|Genome, Fungal|Saccharomyces cerevisiae|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/15.10.776', '10705431', 'The question addressed here is how cooperative interactions among transcription factors (TFs), a very frequent phenomenon in eukaryotic transcriptional regulation, can be used to identify genes that are regulated by one or more TFs with known DNA binding specificities. Cooperativity may be homotypic, involving binding of only one transcription factor to multiple sites in a genes regulatory region. It may also be heterotypic, involving binding of more than one TF. Both types of cooperativity have in common that the binding sites for the respective TFs form tightly linked clusters, groups of binding sites often more closely associated than expected by chance alone.'),
(69656, 1999, 'bio', 'A new method to predict the consensus secondary structure of a set of unaligned RNA sequences', 'Bouthinon, D|Soldano, H', 'Atelier de BioInformatique, Université Paris VI, France. Dominique.Bouthinon@snv.jussieu.fr|Atelier de BioInformatique, Université Paris VI, France. Dominique.Bouthinon@snv.jussieu.fr', 'France|France', 26, 'Algorithms|Base Sequence|Computational Biology|Consensus Sequence|Escherichia coli|Molecular Sequence Data|Nucleic Acid Conformation|RNA|RNA, Bacterial|RNA, Ribosomal, 16S|RNA, Transfer|Repetitive Sequences, Nucleic Acid|Thermodynamics', 'Journal Article', '10.1093/bioinformatics/15.10.785', '10705432', 'To predict the consensus secondary structure, possibly including pseudoknots, of a set of RNA unaligned sequences.'),
(69657, 1999, 'bio', 'FingerPRINTScan: intelligent searching of the PRINTS motif database', 'Scordis, P|Flower, D R|Attwood, T K', 'School of Biological Sciences, University of Manchester, UK. scordis@bioinf.man.ac.uk|School of Biological Sciences, University of Manchester, UK. scordis@bioinf.man.ac.uk|School of Biological Sciences, University of Manchester, UK. scordis@bioinf.man.ac.uk', 'United Kingdom|United Kingdom|United Kingdom', 58, 'Algorithms|Animals|Caenorhabditis elegans|Computational Biology|Databases, Factual|Genome|Genome, Fungal|Saccharomyces cerevisiae|Software', 'Journal Article', '10.1093/bioinformatics/15.10.799', '10705433', 'By identifying an unknown gene or protein as a member of a known family, we can infer a wealth of previously compiled information pertinent to that family and its members.'),
(69658, 1999, 'bio', 'An analysis of the Protein Data Bank in search of temporal and global trends', 'Weissig, H|Bourne, P E', 'San Diego Supercomputer Center, La Jolla, CA, USA.|San Diego Supercomputer Center, La Jolla, CA, USA.', 'United States|United States', 14, 'Computational Biology|Databases, Factual|Humans|Internet|Models, Molecular|Protein Conformation|Proteins|Stereoisomerism|Time Factors', 'Journal Article', '10.1093/bioinformatics/15.10.807', '10705434', 'Biological databases, with their rapidly expanding contents, are indispensable tools in the quest to understand more about biological function. However, a serious user of a database that comprises a large collection of data, collected over a long period, will likely be struck by the inconsistency in reporting individual items of data. This paper takes a critical look at the Protein Data Bank (PDB) to explore the seriousness of the problem in one particular data set and to explore the implications to those actively engaged in comparative analysis of these data.'),
(69659, 1999, 'bio', 'Homonyms and synonyms in the Dictionary of Interfaces in Proteins (DIP)', 'Preissner, R|Goede, A|Frömmel, C', 'Medical Faculty, Humboldt University, Charité, Institute of Biochemistry, Berlin, Germany. preissner@rz.hu-berlin.de|Medical Faculty, Humboldt University, Charité, Institute of Biochemistry, Berlin, Germany. preissner@rz.hu-berlin.de|Medical Faculty, Humboldt University, Charité, Institute of Biochemistry, Berlin, Germany. preissner@rz.hu-berlin.de', 'Germany|Germany|Germany', 7, 'Algorithms|Amino Acid Sequence|Computational Biology|Databases, Factual|Dictionaries, Chemical as Topic|Models, Molecular|Molecular Mimicry|Molecular Sequence Data|Protein Conformation|Proteins', 'Comparative Study', '10.1093/bioinformatics/15.10.832', '10705435', 'Should reports on molecular mimicry in particular cases, e.g. responsible for cross-reactivity, be considered as accidental or as a general principle in protein evolution? To answer this question, two types of similarity have to be considered: those in homologues (synonyms) and resemblance between patches from unrelated proteins (homonyms).'),
(69660, 1999, 'bio', 'bioWidgets: data interaction components for genomics', 'Fischer, S|Crabtree, J|Brunk, B|Gibson, M|Overton, G C', 'Center for Bioinformatics, University of Pennsylvania, Philadelphia 19104, USA. sfischer@pcbi.upenn.edu|Center for Bioinformatics, University of Pennsylvania, Philadelphia 19104, USA. sfischer@pcbi.upenn.edu|Center for Bioinformatics, University of Pennsylvania, Philadelphia 19104, USA. sfischer@pcbi.upenn.edu|Center for Bioinformatics, University of Pennsylvania, Philadelphia 19104, USA. sfischer@pcbi.upenn.edu|Center for Bioinformatics, University of Pennsylvania, Philadelphia 19104, USA. sfischer@pcbi.upenn.edu', 'United States|United States|United States|United States|United States', 0, 'Amino Acid Sequence|Base Sequence|Computational Biology|Computer Graphics|Computer Simulation|DNA|Databases, Factual|Genome|Molecular Sequence Data|Proteins|Sequence Alignment|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/15.10.837', '10705436', 'The presentation of genomics data in a perspicuous visual format is critical for its rapid interpretation and validation. Relatively few public database developers have the resources to implement sophisticated front-end user interfaces themselves. Accordingly, these developers would benefit from a reusable toolkit of user interface and data visualization components.'),
(69661, 1999, 'bio', 'ORBIT: an integrated environment for user-customized bioinformatics tools', 'Bellgard, M I|Hiew, H L|Hunter, A|Wiebrands, M', 'Murdoch Bioinformatics Research Group, School of Information Technology, Murdoch University, Australia.|Murdoch Bioinformatics Research Group, School of Information Technology, Murdoch University, Australia.|Murdoch Bioinformatics Research Group, School of Information Technology, Murdoch University, Australia.|Murdoch Bioinformatics Research Group, School of Information Technology, Murdoch University, Australia.', 'Australia|Australia|Australia|Australia', 4, 'Computational Biology|Internet|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/15.10.847', '10705437', 'There are a large number of computational programs freely available to bioinformaticians via a client/server, web-based environment. However, the client interface to these tools (typically an html form page) cannot be customized from the client side as it is created by the service provider. The form page is usually generic enough to cater for a wide range of users. However, this implies that a user cannot set as default advanced program parameters on the form or even customize the interface to his/her specific requirements or preferences. Currently, there is a lack of end-user interface environments that can be modified by the user when accessing computer programs available on a remote server running on an intranet or over the Internet.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(69662, 1999, 'bio', 'MUTbase: maintenance and analysis of distributed mutation databases', 'Riikonen, P|Vihinen, M', 'Department of Computer Science, University of Turku, Finland.|Department of Computer Science, University of Turku, Finland.', 'Finland|Finland', 46, 'Algorithms|Amino Acid Sequence|Base Sequence|Computational Biology|DNA|DNA Restriction Enzymes|Databases, Factual|Internet|Molecular Sequence Data|Mutation|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/15.10.852', '10705438', 'To develop tools for the submission of mutations to databases and maintenance of locus-specific mutation databases. Advanced, integrated computer systems are needed to store and organize the increasing mutation information.'),
(69663, 1999, 'bio', 'Completing the E coli proteome: a database of gene products characterised since the completion of the genome sequence', 'Thomas, G H', 'Department of Molecular Microbiology, John Innes Centre, Norwich, Norfolk, UK. gav.thomas@bbsrc.ac.uk', 'United Kingdom', 0, 'Bacterial Proteins|Computational Biology|Databases, Factual|Escherichia coli|Genome, Bacterial|Internet|Proteome', 'Journal Article', '10.1093/bioinformatics/15.10.860', '10705439', 'A database collating research on E. coli genes whose products have been characterised subsequent to in silico predictions from the completed genome sequence.'),
(69664, 1999, 'bio', 'MULTICLUSTAL: a systematic method for surveying Clustal W alignment parameters', 'Yuan, J|Amend, A|Borkowski, J|DeMarco, R|Bailey, W|Liu, Y|Xie, G|Blevins, R', 'Merck and Co., Inc., Department of Bioinformatics, Rahway, NJ 07065, USA. jeffrey_yuan@merck.com|Merck and Co., Inc., Department of Bioinformatics, Rahway, NJ 07065, USA. jeffrey_yuan@merck.com|Merck and Co., Inc., Department of Bioinformatics, Rahway, NJ 07065, USA. jeffrey_yuan@merck.com|Merck and Co., Inc., Department of Bioinformatics, Rahway, NJ 07065, USA. jeffrey_yuan@merck.com|Merck and Co., Inc., Department of Bioinformatics, Rahway, NJ 07065, USA. jeffrey_yuan@merck.com|Merck and Co., Inc., Department of Bioinformatics, Rahway, NJ 07065, USA. jeffrey_yuan@merck.com|Merck and Co., Inc., Department of Bioinformatics, Rahway, NJ 07065, USA. jeffrey_yuan@merck.com|Merck and Co., Inc., Department of Bioinformatics, Rahway, NJ 07065, USA. jeffrey_yuan@merck.com', 'United States|United States|United States|United States|United States|United States|United States|United States', 25, 'Amino Acid Sequence|Computational Biology|Databases, Factual|Molecular Sequence Data|Proteins|Sequence Alignment|Software|src Homology Domains', 'Journal Article', '10.1093/bioinformatics/15.10.862', '10705440', 'MULTICLUSTAL is a Perl script designed to automate the process of alignment parameter choice for Clustal W with the goal of generating high quality multiple sequence alignments.'),
(69665, 1999, 'bio', 'The Second Georgia Tech International Conference on Bioinformatics: Sequence, Structure and Function November 11-14, 1999, Atlanta, Georgia, USA Proceedings', '-', '-', '-', 0, 'Animals|Computational Biology|Humans|Sequence Alignment|Sequence Analysis', 'Congress', '10.1093/bioinformatics/15.10.862', '10743552', '-'),
(69666, 1999, 'bio', 'FramePlus: aligning DNA to protein sequences', 'Halperin, E|Faigler, S|Gill-More, R', 'Compugen Ltd., Tel Aviv, Israel.|Compugen Ltd., Tel Aviv, Israel.|Compugen Ltd., Tel Aviv, Israel.', 'Israel|Israel|Israel', 0, 'Algorithms|Computational Biology|Computer Communication Networks|Evaluation Studies as Topic|Expressed Sequence Tags|Frameshifting, Ribosomal|Predictive Value of Tests|Sensitivity and Specificity|Sequence Alignment|Sequence Analysis, DNA|Sequence Analysis, Protein|Software Validation', 'Comparative Study', '10.1093/bioinformatics/15.11.867', '10743553', 'Automated annotation of Expressed Sequence Tags (ESTs) is becoming increasingly important as EST databases continue to grow rapidly. A common approach to annotation is to align the gene fragments against well-documented databases of protein sequences. The sensitivity of the alignment algorithm is key to the success of such methods.'),
(69667, 1999, 'bio', 'Finding prokaryotic genes by the frame-by-frame algorithm: targeting gene starts and overlapping genes', 'Shmatkov, A M|Melikyan, A A|Chernousko, F L|Borodovsky, M', 'Russian Academy of Science, Institute for Problems in Mechanics, Moscow, Russia.|Russian Academy of Science, Institute for Problems in Mechanics, Moscow, Russia.|Russian Academy of Science, Institute for Problems in Mechanics, Moscow, Russia.|Russian Academy of Science, Institute for Problems in Mechanics, Moscow, Russia.', '-|-|-|-', 39, 'Algorithms|Bacteria|Codon, Initiator|Computational Biology|Databases, Factual|Evaluation Studies as Topic|Genes, Bacterial|Genes, Overlapping|Genome, Bacterial|Models, Genetic|Open Reading Frames|Protein Biosynthesis|Reproducibility of Results|Sensitivity and Specificity|Sequence Analysis, DNA|Software Validation', 'Comparative Study', '10.1093/bioinformatics/15.11.874', '10743554', 'Tightly packed prokaryotic genes frequently overlap with each other. This feature, rarely seen in eukaryotic DNA, makes detection of translation initiation sites and, therefore, exact predictions of prokaryotic genes notoriously difficult. Improving the accuracy of precise gene prediction in prokaryotic genomic DNA remains an important open problem.'),
(69668, 1999, 'bio', 'Evaluation of gene prediction software using a genomic data set: application to Arabidopsis thaliana sequences', 'Pavy, N|Rombauts, S|Déhais, P|Mathé, C|Ramana, D V|Leroy, P|Rouzé, P', 'Laboratoire associé de lINRA, France.|Laboratoire associé de lINRA, France.|Laboratoire associé de lINRA, France.|Laboratoire associé de lINRA, France.|Laboratoire associé de lINRA, France.|Laboratoire associé de lINRA, France.|Laboratoire associé de lINRA, France.', 'France|France|France|France|France|France|France', 72, 'Alternative Splicing|Arabidopsis|Computational Biology|Contig Mapping|Databases, Factual|Evaluation Studies as Topic|Exons|Genome, Plant|Models, Genetic|Reproducibility of Results|Sequence Analysis, DNA|Sequence Analysis, Protein|Software Validation', 'Comparative Study', '10.1093/bioinformatics/15.11.887', '10743555', 'The annotation of the Arabidopsis thaliana genome remains a problem in terms of time and quality. To improve the annotation process, we want to choose the most appropriate tools to use inside a computer-assisted annotation platform. We therefore need evaluation of prediction programs with Arabidopsis sequences containing multiple genes.'),
(69669, 1999, 'bio', 'An automated comparative analysis of 17 complete microbial genomes', 'Bansal, A K', 'Department of Mathematics and Computer Science, Kent State University, OH 44242, USA.', 'United States', 44, 'Algorithms|Computational Biology|Conserved Sequence|Databases, Factual|Gene Duplication|Genes, Bacterial|Genes, Overlapping|Genome, Bacterial|Models, Genetic|Multigene Family|Sequence Alignment|Sequence Analysis, DNA', 'Comparative Study', '10.1093/bioinformatics/15.11.900', '10743556', 'As sequenced genomes become larger and sequencing becomes faster, there is a need to develop accurate automated genome comparison techniques and databases to facilitate derivation of genome functionality, identification of enzymes, putative operons and metabolic pathways, and to derive phylogenetic classification of microbes.'),
(69670, 1999, 'bio', 'Genome rearrangement with gene families', 'Sankoff, D', 'Centre de recherches mathématiques, Université de Montréal, Québec, Canada.', 'Canada', 0, 'Algorithms|Computational Biology|Computer Simulation|Evolution, Molecular|Gene Duplication|Genome|Models, Genetic|Multigene Family|Phylogeny|Sequence Alignment', 'Journal Article', '10.1093/bioinformatics/15.11.909', '10743557', 'The theory and practice of genome rearrangement analysis breaks down in the biologically widespread contexts where each gene may be present in a number of copies, not necessarily contiguous. In some of these contexts it is, however, appropriate to ask which members of each gene family in two genomes G and H, lengths lG and lH, are its true exemplars, i.e. which best reflect the original position of the ancestral gene in the common ancestor genome. This entails a search for the two exemplar strings of same length n (= number of gene families, including singletons), having the smallest possible rearrangement distance: the exemplar distance.'),
(69671, 1999, 'bio', 'Structural basis for triplet repeat disorders: a computational analysis', 'Baldi, P|Brunak, S|Chauvin, Y|Pedersen, A G', 'Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425, USA.|Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425, USA.|Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425, USA.|Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425, USA.', 'United States|United States|United States|United States', 23, 'Anticipation, Genetic|Carrier Proteins|Computer Simulation|DNA|Deoxyribonuclease I|Genetic Diseases, Inborn|Humans|Models, Genetic|Multiple System Atrophy|Nerve Tissue Proteins|Nucleic Acid Conformation|Nucleosomes|Pliability|Protein Binding|Trinucleotide Repeat Expansion|Trinucleotide Repeats', 'Journal Article', '10.1093/bioinformatics/15.11.918', '10743558', 'Over a dozen major degenerative disorders, including myotonic distrophy, Huntingtons disease and fragile X syndrome, result from unstable expansions of particular trinucleotides. Remarkably, only some of all the possible triplets, namely CAG/CTG, CGG/CCG and GAA/TTC, have been associated with the known pathological expansions. This raises some basic questions at the DNA level. Why do particular triplets seem to be singled out? What is the mechanism for their expansion and how does it depend on the triplet itself? Could other triplets or longer repeats be involved in other diseases?'),
(69672, 1999, 'bio', 'A simple algorithm for detecting circular permutations in proteins', 'Uliel, S|Fliess, A|Amir, A|Unger, R', 'Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.|Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.|Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.|Faculty of Life Sciences, Bar-Ilan University, Ramat-Gan, Israel.', 'Israel|Israel|Israel|Israel', 45, 'Algorithms|Computational Biology|Computer Simulation|Data Display|Databases, Factual|Evaluation Studies as Topic|Evolution, Molecular|Lectins|Models, Genetic|Proteins|Sequence Alignment|Sequence Analysis, Protein|Time Factors', 'Journal Article', '10.1093/bioinformatics/15.11.930', '10743559', 'Circular permutation of a protein is a genetic operation in which part of the C-terminal of the protein is moved to its N-terminal. Recently, it has been shown that proteins that undergo engineered circular permutations generally maintain their three dimensional structure and biological function. This observation raises the possibility that circular permutation has occurred in Nature during evolution. In this scenario a protein underwent circular permutation into another protein, thereafter both proteins further diverged by standard genetic operations. To study this possibility one needs an efficient algorithm that for a given pair of proteins can detect the underlying event of circular permutations. A possible formal description of the question is: given two sequences, find a circular permutation of one of them under which the edit distance between the proteins is minimal. A naive algorithm might take time proportional to N3 or even N4, which is prohibitively slow for a large-scale survey. A sophisticated algorithm that runs in asymptotic time of N2 was recently suggested, but it is not practical for a large-scale survey.'),
(69673, 1999, 'bio', 'Exploiting the past and the future in protein secondary structure prediction', 'Baldi, P|Brunak, S|Frasconi, P|Soda, G|Pollastri, G', 'Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425, USA.|Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425, USA.|Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425, USA.|Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425, USA.|Department of Information and Computer Science, College of Medicine, University of California, Irvine 92697-3425, USA.', 'United States|United States|United States|United States|United States', 0, 'Algorithms|Computational Biology|Computer Simulation|Evaluation Studies as Topic|Models, Genetic|Neural Networks (Computer)|Predictive Value of Tests|Protein Structure, Secondary|Reproducibility of Results|Software Validation', 'Journal Article', '10.1093/bioinformatics/15.11.937', '10743560', 'Predicting the secondary structure of a protein (alpha-helix, beta-sheet, coil) is an important step towards elucidating its three-dimensional structure, as well as its function. Presently, the best predictors are based on machine learning approaches, in particular neural network architectures with a fixed, and relatively short, input window of amino acids, centered at the prediction site. Although a fixed small window avoids overfitting problems, it does not permit capturing variable long-rang information.'),
(69674, 1999, 'bio', 'Local multiple sequence alignment using dead-end elimination', 'Lukashin, A V|Rosa, J J', 'Biogen, Inc., Cambridge, MA 02142, USA.|Biogen, Inc., Cambridge, MA 02142, USA.', 'United States|United States', 0, 'Algorithms|Computational Biology|Evaluation Studies as Topic|Predictive Value of Tests|Reproducibility of Results|Sequence Alignment|Sequence Analysis, Protein|Sequence Homology, Amino Acid|Time Factors', 'Journal Article', '10.1093/bioinformatics/15.11.947', '10743561', 'Local multiple sequence alignment is a basic tool for extracting functionally important regions shared by a family of protein sequences. We present an effectively polynomial-time algorithm for rigorously solving the local multiple alignment problem.'),
(69675, 1999, 'bio', 'Polymer chromosome models and Monte Carlo simulations of radiation breaking DNA', 'Ponomarev, A L|Sachs, R K', 'Department of Mathematics, University of California, Berkeley 94720, USA. alp17@math.berkeley.edu|Department of Mathematics, University of California, Berkeley 94720, USA. alp17@math.berkeley.edu', 'United States|United States', 0, 'Algorithms|Animals|Chromatin|Chromosome Breakage|Computer Simulation|Cricetinae|Cricetulus|DNA|DNA Damage|Models, Genetic|Monte Carlo Method|Software Validation', 'Journal Article', '10.1093/bioinformatics/15.12.957', '10745984', 'Chromatin breakage by ionizing radiation is relevant to studies of carcinogenesis, tumor radiotherapy, biodosimetry and molecular biology. This article focuses on computer analysis of chromosome irradiation in mammlian cells.'),
(69676, 1999, 'bio', 'IMAGEne I: clustering and ranking of IMAGE cDNA clones corresponding to known genes', 'Cariaso, M|Folta, P|Wagner, M|Kuczmarski, T|Lennon, G', 'Biology and Biotechnology Program, Lawrence Livermore National Laboratory, CA 94550, USA.|Biology and Biotechnology Program, Lawrence Livermore National Laboratory, CA 94550, USA.|Biology and Biotechnology Program, Lawrence Livermore National Laboratory, CA 94550, USA.|Biology and Biotechnology Program, Lawrence Livermore National Laboratory, CA 94550, USA.|Biology and Biotechnology Program, Lawrence Livermore National Laboratory, CA 94550, USA.', 'United States|United States|United States|United States|United States', 9, 'Algorithms|Animals|Cloning, Molecular|DNA, Complementary|Data Collection|Data Display|Databases, Factual|Humans|Information Storage and Retrieval|Internet|Mice|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/15.12.965', '10745985', 'To enhance the usefulness of the I.M.A.G.E. Consortium (Lennon et al., 1996, Genomics, 33, 151-152) cDNA clone collection by directed analysis and organization of their associated Expressed Sequence Tags (ESTs), thus enabling effective mining of the immense amounts of public cDNA information.'),
(69677, 1999, 'bio', 'SEGMENT: identifying compositional domains in DNA sequences', 'Oliver, J L|Román-Roldán, R|Pérez, J|Bernaola-Galván, P', 'Department of Genetics, Faculty of Sciences, University of Granada, Spain. oliver@ugr.es|Department of Genetics, Faculty of Sciences, University of Granada, Spain. oliver@ugr.es|Department of Genetics, Faculty of Sciences, University of Granada, Spain. oliver@ugr.es|Department of Genetics, Faculty of Sciences, University of Granada, Spain. oliver@ugr.es', 'Spain|Spain|Spain|Spain', 0, 'Algorithms|Data Display|Escherichia coli|Mathematical Computing|Models, Genetic|Molecular Structure|Protein Structure, Tertiary|Sequence Analysis, DNA|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/15.12.974', '10745986', 'DNA sequences are formed by patches or domains of different nucleotide composition. In a few simple sequences, domains can simply be identified by eye, however, most DNA sequences show a complex compositional heterogeneity (fractal structure), which cannot be properly detected by current methods. Recently, a computationally efficient segmentation method to analyse such nonstationary sequence structures, based on the Jensen-Shannon entropic divergence, has been described. Specific algorithms implementing this method are now needed.'),
(69678, 1999, 'bio', 'Segmentation of yeast DNA using hidden Markov models', 'Peshkin, L|Gelfand, M S', 'Brown University, Providence, RI 02912, USA. ldp@cs.brown.edu|Brown University, Providence, RI 02912, USA. ldp@cs.brown.edu', 'United States|United States', 0, 'Algorithms|DNA|Hydrogen|Markov Chains|Models, Genetic|Models, Statistical|Saccharomyces cerevisiae|Sequence Analysis, DNA', 'Journal Article', '10.1093/bioinformatics/15.12.980', '10745987', 'Compositionally homogeneous segments of genomic DNA often correspond to meaningful biological units. Simple sliding window analysis is usually insufficient for compositional segmentation of natural sequences. Hidden Markov models (HMM) with a small number of states are a natural language for description of compositional properties of chromosome-size DNA sequences.'),
(69679, 1999, 'bio', 'Modeling and predicting transcriptional units of Escherichia coli genes using hidden Markov models', 'Yada, T|Nakao, M|Totoki, Y|Nakai, K', 'Genomic Sciences Center, RIKEN, c/o Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan.|Genomic Sciences Center, RIKEN, c/o Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan.|Genomic Sciences Center, RIKEN, c/o Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan.|Genomic Sciences Center, RIKEN, c/o Laboratory of Genome Database, Human Genome Center, Institute of Medical Science, University of Tokyo, Japan.', 'Japan|Japan|Japan|Japan', 0, 'Algorithms|Base Sequence|Binding Sites|Escherichia coli|Markov Chains|Models, Genetic|Models, Statistical|Predictive Value of Tests|Ribosomes|Transcription, Genetic', 'Journal Article', '10.1093/bioinformatics/15.12.987', '10745988', 'The hidden Markov model (HMM) is a valuable technique for gene-finding, especially because its flexibility enables the inclusion of various sequence features. Recent programs for bacterial gene-finding include the information of ribosomal binding site (RBS) to improve the recognition accuracy of the start codon, using this feature. We report here our attempt to extend the model into the total transcriptional unit, enabling the prediction of operon structures.'),
(69680, 1999, 'bio', 'On the complexity measures of genetic sequences', 'Gusev, V D|Nemytikova, L A|Chuzhanova, N A', 'Institute of Mathematics, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia. gusev@math.nsc.ru|Institute of Mathematics, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia. gusev@math.nsc.ru|Institute of Mathematics, Siberian Branch of Russian Academy of Science, Novosibirsk, Russia. gusev@math.nsc.ru', '-|-|-', 120, 'Algorithms|Base Sequence|Growth Hormone|Humans|Information Storage and Retrieval|Models, Genetic|Repetitive Sequences, Nucleic Acid|Sequence Analysis, DNA|Sequence Homology, Amino Acid', 'Journal Article', '10.1093/bioinformatics/15.12.994', '10745989', 'It is well known that the regulatory regions of genomes are highly repetitive. They are rich in direct, symmetric and complemented repeats, and there is no doubt about the functional significance of these repeats. Among known measures of complexity, the Ziv-Lempel complexity measure reflects most adequately repeats occurring in the text. But this measure does not take into account isomorphic repeats. By isomorphic repeats we mean fragments that are identical (or symmetric) modulo some permutation of the alphabet letters.'),
(69681, 1999, 'bio', 'IMPALA: matching a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices', 'Schäffer, A A|Wolf, Y I|Ponting, C P|Koonin, E V|Aravind, L|Altschul, S F', 'National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. schaffer@helix.nih.gov|National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. schaffer@helix.nih.gov|National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. schaffer@helix.nih.gov|National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. schaffer@helix.nih.gov|National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. schaffer@helix.nih.gov|National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA. schaffer@helix.nih.gov', 'United States|United States|United States|United States|United States|United States', 252, 'Algorithms|Bacterial Proteins|Databases, Factual|False Negative Reactions|False Positive Reactions|Information Storage and Retrieval|Odds Ratio|Sequence Alignment|Sequence Analysis, Protein|Sequence Homology|Software', 'Journal Article', '10.1093/bioinformatics/15.12.1000', '10745990', 'Many studies have shown that database searches using position-specific score matrices (PSSMs) or profiles as queries are more effective at identifying distant protein relationships than are searches that use simple sequences as queries. One popular program for constructing a PSSM and comparing it with a database of sequences is Position-Specific Iterated BLAST (PSI-BLAST).'),
(69682, 1999, 'bio', 'Post-processing long pairwise alignments', 'Zhang, Z|Berman, P|Wiehe, T|Miller, W', 'Department of Computer Science and Engineering, Pennsylvania State University, University Park 16802, USA.|Department of Computer Science and Engineering, Pennsylvania State University, University Park 16802, USA.|Department of Computer Science and Engineering, Pennsylvania State University, University Park 16802, USA.|Department of Computer Science and Engineering, Pennsylvania State University, University Park 16802, USA.', 'United States|United States|United States|United States', 0, 'Algorithms|Animals|Humans|Mice|Mutation|Sequence Alignment|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/15.12.1012', '10745991', 'The local alignment problem for two sequences requires determining similar regions, one from each sequence, and aligning those regions. For alignments computed by dynamic programming, current approaches for selecting similar regions may have potential flaws. For instance, the criterion of Smith and Waterman can lead to inclusion of an arbitrarily poor internal segment. Other approaches can generate an alignment scoring less than some of its internal segments.'),
(69683, 1999, 'bio', 'Browsing protein families via the Rich Family Description format', 'Corpet, F|Gouzy, J|Kahn, D', 'Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, Castanet, France. fcorpet@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, Castanet, France. fcorpet@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, Castanet, France. fcorpet@toulouse.inra.fr', 'France|France|France', 0, 'Algorithms|Data Display|Databases, Factual|Information Storage and Retrieval|Internet|Phylogeny|Sequence Alignment|Sequence Analysis, Protein|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/15.12.1020', '10745992', 'Multiple alignments of protein sequences are the basis of structural and functional analysis of protein families. It is however difficult even for an expert biologist to comprehend an alignment of more than 50 to 100 homologous sequences.'),
(69684, 1999, 'bio', 'PHYSEAN: PHYsical SEquence ANalysis for the identification of protein domains on the basis of physical and chemical properties of amino acids', 'Ladunga, I', 'SmithKline Beecham Pharmaceuticals, Bioinformatics Department, King of Prussia, PA 19406-0939, USA. Steve_Ladunga@sbphrd.com', 'United States', 17, 'Algorithms|Amino Acid Sequence|Amino Acids|Chemical Phenomena|Chemistry, Physical|Cytosol|Neural Networks (Computer)|Protein Sorting Signals|Protein Structure, Tertiary|Sequence Alignment|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/15.12.1028', '10745993', 'PHYSEAN predicts protein classes with highly variable sequences on the basis of their physical, chemical and biological characteristics such as diverse hydrophobicity, structural propensity and steric properties. These characteristics, calculated from multiple positions in a sequence, may be conserved even between sequences that fail to produce alignments at any acceptable level of statistical significance. PHYSEAN complements methods that require sequence alignments (BLAST, FASTA, dynamic programming) by adding less residue- and position-specific physicochemical information on the protein or the domain.'),
(69685, 1999, 'bio', 'Decision tree-based formation of consensus protein secondary structure prediction', 'Selbig, J|Mevissen, T|Lengauer, T', 'Institute for Algorithms and Scientific Computing (SCAI), GMD-German National Research Center for Information Technology, Sankt Augustin, Germany.|Institute for Algorithms and Scientific Computing (SCAI), GMD-German National Research Center for Information Technology, Sankt Augustin, Germany.|Institute for Algorithms and Scientific Computing (SCAI), GMD-German National Research Center for Information Technology, Sankt Augustin, Germany.', 'Germany|Germany|Germany', 40, 'Algorithms|Artificial Intelligence|Decision Trees|Protein Structure, Secondary|Reproducibility of Results|Systems Integration', 'Journal Article', '10.1093/bioinformatics/15.12.1039', '10745994', 'Prediction of protein secondary structure provides information that is useful for other prediction methods like fold recognition and ab initio 3D prediction. A consensus prediction constructed from the output of several methods should yield more reliable results than each of the individual methods.'),
(69686, 1999, 'bio', 'Ontology for immunogenetics: the IMGT-ONTOLOGY', 'Giudicelli, V|Lefranc, M P', 'Laboratoire dImmunoGénétique Moléculaire, UPR CNRS 1142, Institut de Génétique Humaine, Montpellier, France.|Laboratoire dImmunoGénétique Moléculaire, UPR CNRS 1142, Institut de Génétique Humaine, Montpellier, France.', 'France|France', 36, 'Animals|Artificial Intelligence|Databases, Factual|Humans|Immunogenetics|Quality Control|Reproducibility of Results|Software Design|Systems Integration|User-Computer Interface|Vocabulary, Controlled', 'Journal Article', '10.1093/bioinformatics/15.12.1047', '10745995', 'IMGT, the international ImMunoGeneTics database (http:@imgt.cines.fr:8104), created by M.-P. Lefranc, is an integrated database specializing in antigen receptors (immunoglobulins and T-cell receptors) and major histocompatibility complex (MHC) of all vertebrate species. IMGT accurate immunogenetics data are based on the standardization of the biological knowledge provided by the ImMunoGeneTics IMGT-ONTOLOGY. The IMGT-ONTOLOGY describes the classification and specification of terms needed for immunogenetics and bioinformatics. IMGT-ONTOLOGY covers four main concepts: IDENTIFICATION, DESCRIPTION, CLASSIFICATION and OBTENTION. These concepts allow an extensive and standardized description and characterization of immunoglobulin and T-cell receptor data. The controlled vocabulary and the annotation rules are indispensable to ensure accuracy, consistency and coherence in IMGT. IMGT-ONTOLOGY allows scientists and clinicians to use, for the first time, identical terms with the same meaning in immunogenetics. It provides a semantic repository that will improve interoperability between specialist and generalist databases.'),
(69687, 1999, 'bio', 'A plant calmodulin-binding motor is part kinesin and part myosin', 'Reddy, V S|Reddy, A S', 'Department of Biology, Colorado State University, Fort Collins 80523, USA.|Department of Biology, Colorado State University, Fort Collins 80523, USA.', 'United States|United States', 0, 'Amino Acid Sequence|Arabidopsis|Arabidopsis Proteins|Calmodulin|Calmodulin-Binding Proteins|Humans|Kinesin|Molecular Motor Proteins|Molecular Sequence Data|Mutation|Myosins|Plant Proteins|Plants|Sequence Alignment', 'Journal Article', '10.1093/bioinformatics/15.12.1055', '10745996', '-'),
(69688, 1999, 'bio', 'Shufflet: shuffling sequences while conserving the k-let counts', 'Coward, E', 'Laboratoire Génome et Informatique, Université de Versailles Saint-Quentin-en-Yvelines, France. coward@genetique.uvsq.fr', 'France', 24, 'Algorithms|Databases, Factual|Information Storage and Retrieval|Internet|Models, Statistical|Monte Carlo Method|Programming Languages|Sequence Analysis, DNA|Stochastic Processes', 'Journal Article', '10.1093/bioinformatics/15.12.1058', '10745997', 'Shufflet is a program and a web-application that generates fast random shufflings of sequences (DNA, protein or others), conserving the exact k-let counts for a given k. The sequences are sampled uniformly from all the valid permutations.'),
(69689, 1999, 'bio', 'ModBase: a database of comparative protein structure models', 'Sánchez, R|Sali, A', 'Pels Family Center for Biochemistry and Structural Biology, Rockefeller University, New York, NY 10021, USA.|Pels Family Center for Biochemistry and Structural Biology, Rockefeller University, New York, NY 10021, USA.', 'United States|United States', 32, 'Bacterial Proteins|Databases, Factual|Information Storage and Retrieval|Internet|Models, Genetic|Protein Folding|Sequence Alignment|Sequence Analysis, DNA', 'Journal Article', '10.1093/bioinformatics/15.12.1060', '10745998', 'ModBase is a database of evaluated and annotated comparative protein structure models. The database also includes fold assignments and alignments on which the models were based.'),
(69690, 1999, 'bio', 'A platform for integrating threading results with protein family analyses', 'Pazos, F|Rost, B|Valencia, A', 'Protein Design Group, CNB-CSIC, Cantoblanco, Madrid, Spain.|Protein Design Group, CNB-CSIC, Cantoblanco, Madrid, Spain.|Protein Design Group, CNB-CSIC, Cantoblanco, Madrid, Spain.', 'Spain|Spain|Spain', 0, 'Chromosome Mapping|Data Display|Databases, Factual|Internet|Models, Genetic|Mutation|Protein Conformation|Protein Folding|Protein Structure, Secondary|Sequence Alignment|Sequence Analysis, DNA|Software|Systems Integration|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/15.12.1062', '10745999', 'We have developed a package for the interactive visualization of results from different threading programs. Additionally, we have integrated relevant information about protein sequence, function, evolution, and structure into the interface.'),
(69691, 1999, 'bio', 'Sausage: protein threading with flexible force fields', 'Huber, T|Russell, A J|Ayers, D|Torda, A E', 'Research School of Chemistry, Australian National University, Canberra, Australia.|Research School of Chemistry, Australian National University, Canberra, Australia.|Research School of Chemistry, Australian National University, Canberra, Australia.|Research School of Chemistry, Australian National University, Canberra, Australia.', 'Australia|Australia|Australia|Australia', 2, 'Algorithms|Artificial Intelligence|Databases, Factual|Protein Folding|Proteins|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/15.12.1064', '10746000', 'Sausage is a protein sequence threading program, but with remarkable run-time flexibility. Using different scripts, it can calculate protein sequence-structure alignments, search structure libraries, swap force fields, create models from alignments, convert file formats and analyse results. There are several different force fields which might be classed as knowledge-based, although they do not rely on Boltzmann statistics. Different force fields are used for alignment calculations and subsequent ranking of calculated models.'),
(69692, 1999, 'bio', 'Representation of functional information in the SWISS-PROT data bank', 'Junker, V L|Apweiler, R|Bairoch, A', 'European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, UK. junker@ebi.ac.uk|European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, UK. junker@ebi.ac.uk|European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambs, UK. junker@ebi.ac.uk', 'United Kingdom|United Kingdom|United Kingdom', 36, 'Databases, Factual|Documentation|Information Storage and Retrieval|Internet|Proteins|Sequence Analysis', 'Journal Article', '10.1093/bioinformatics/15.12.1066', '10746001', 'Functional information in SWISS-PROT results, primarily, from assessment of articles reporting characterization. Predicted information is labeled with flags describing the evidence level (e.g. potential, probable, by similarity).'),
(69693, 1999, 'bio', 'WebPHYLIP: a web interface to PHYLIP', 'Lim, A|Zhang, L', 'BioInformatics Centre, National University of Singapore.|BioInformatics Centre, National University of Singapore.', 'Singapore|Singapore', 0, 'Data Display|Information Storage and Retrieval|Internet|Phylogeny|Programming Languages|Software|Software Design|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/15.12.1068', '10746002', 'A web interface to PHYLIP (version 3.57 C) is implemented using CGI/Perl programming. It enables users to do phylogenetic analysis through the Internet.'),
(69694, 2000, 'bio', 'The early days of bioinformatics publishing', 'Roberts, R J', 'New England Biolabs, Beverly, MA 01915, USA. roberts@neb.com', 'United States', 5, 'Computational Biology|Databases, Factual|History, 20th Century|Humans|Periodicals as Topic|Publishing|Software', 'Historical Article', '10.1093/bioinformatics/16.1.2', '10812470', 'A brief history of the early days of publishing in the bioinformatics field is presented.'),
(69695, 2000, 'bio', 'Earliest pages of bioinformatics', 'Trifonov, E N', 'Department of Structural Biology, Weizmann Institute of Science, Rehovot, Israel. edward.trifonov@weizmann.ac.il', 'Israel', 11, 'Animals|Codon|Computational Biology|Gene Expression Regulation|History, 19th Century|History, 20th Century|Humans|Protein Biosynthesis|RNA Splicing|Research|Sequence Analysis', 'Historical Article', '10.1093/bioinformatics/16.1.5', '10812471', 'This review is a brief outline of the chronology and essence of early events in bioinformatics, covering the period from 1869 (discovery of DNA by Miescher) to 1980-1981 (beginning of massive sequencing). For the purpose of this review, bioinformatics is understood as a chapter of molecular biology dealing with the amino acid and nucleotide sequences and with the information they carry.'),
(69696, 2000, 'bio', 'A historical perspective on gene/protein functional assignment', 'Hodgman, T C', 'GlaxoWellcome Medicines Research Centre, Stevenage, UK. ch18380@ggr.co.uk', 'United Kingdom', 0, 'Genes|History, 20th Century|Humans|Proteins|Research|Sequence Alignment|Sequence Analysis', 'Historical Article', '10.1093/bioinformatics/16.1.10', '10812472', 'Sequence determination and analysis began on proteins in the 1950s, with RNA starting about a decade later and DNA a similar period later still. Hence many of the concepts for function prediction were first developed by looking at amino acid sequences. Over time these methods have become much more sophisticated, allowing better discrimination of only weak similarities. The most recent developments concern an examination of contextual information, such as operon structure, metabolic reconstruction or co-expression profiles.'),
(69697, 2000, 'bio', 'DNA binding sites: representation and discovery', 'Stormo, G D', 'Department of Genetics, Washington University Medical School, St. Louis, MO 63110, USA. stormo@ural.wustl.edu', 'United States', 0, 'Binding Sites|DNA|DNA-Binding Proteins|History, 20th Century|Research', 'Historical Article', '10.1093/bioinformatics/16.1.16', '10812473', 'The purpose of this article is to provide a brief history of the development and application of computer algorithms for the analysis and prediction of DNA binding sites. This problem can be conveniently divided into two subproblems. The first is, given a collection of known binding sites, develop a representation of those sites that can be used to search new sequences and reliably predict where additional binding sites occur. The second is, given a set of sequences known to contain binding sites for a common factor, but not knowing where the sites are, discover the location of the sites in each sequence and a representation for the specificity of the protein.'),
(69698, 2000, 'bio', 'On the trail of protein sequences', 'Doolittle, R F', 'Center for Molecular Genetics, University of California, San Diego, La Jolla 92093-0634, USA. rdoolittle@ucsd.edu', 'United States', 4, 'Animals|Fibrinogen|Fibronectins|History, 20th Century|Humans|Proteins|Research Support as Topic|Sequence Analysis|Sequence Homology, Amino Acid', 'Historical Article', '10.1093/bioinformatics/16.1.24', '10812474', '-'),
(69699, 2000, 'bio', 'History of the enzyme nomenclature system', 'Tipton, K|Boyce, S', 'Department of Biochemistry, Trinity College, Dublin, Ireland. ktipton@tcd.ie|Department of Biochemistry, Trinity College, Dublin, Ireland. ktipton@tcd.ie', 'Ireland|Ireland', 81, 'Enzymes|History, 19th Century|History, 20th Century|Terminology as Topic', 'Historical Article', '10.1093/bioinformatics/16.1.34', '10812475', 'Naming things is essential for people to understand one another, no matter what language or field of interest is involved. This is as true for enzymes, genes and chemicals as it is for birds, food, flowers, etc. Effective communication requires a lack of ambiguity, but, in practice, ambiguities abound even between people who use the same language in different parts of the world, or even within the same country. Whereas ambiguities in the words used for common objects or actions have been the basis for many, more-or-less memorable jokes, they can also cause a great deal of confusion. Such linguistic chaos is welcomed by many as being a part of a diverse heritage that should be preserved at all costs to prevent us from descending into Orwellian newspeak. However, in the sciences, there are distinct advantages in others being able to understand what one is doing. Many groups have stressed the need for standardized, universally accepted systems of nomenclature in chemistry, genetics, enzymology, etc. However, it is the universal acceptance that usually causes the problem. It is rare to find people who will admit that they find nomenclature to be an interesting subject, but many who profess contempt for it will get very excited if it is suggested that their pet nomenclature should be changed in the interest of clarity or uniformity. This account will consider the development of the enzyme nomenclature system, its benefits, shortcomings and future prospects.'),
(69700, 2000, 'bio', 'The early introduction of dynamic programming into computational biology', 'Sankoff, D', 'Centre de recherches mathématiques, Université de Montréal, Québec, Canada. sankoff@ere.umontreal.ca', 'Canada', 33, 'Computational Biology|History, 20th Century|Nucleic Acid Conformation|Phylogeny|RNA|Sequence Alignment|Software', 'Historical Article', '10.1093/bioinformatics/16.1.41', '10812476', '-'),
(69701, 2000, 'bio', 'Serendipity in bioinformatics, the tribulations of a Swiss bioinformatician through exciting times!', 'Bairoch, A', 'Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva, Switzerland. bairoch@cmu.unige.ch', 'Switzerland', 0, 'Computational Biology|Computers|Databases, Factual|Genome, Bacterial|History, 20th Century|Proteome|Software|Switzerland', 'Autobiography', '10.1093/bioinformatics/16.1.48', '10812477', '-'),
(69702, 2000, 'bio', 'A brief history of genome research and bioinformatics in France', 'Danchin, A', 'Regulation of Gene Expression, Institut Pasteur, Paris, France. adanchin@pasteur.fr', 'France', 2, 'Computational Biology|Forecasting|France|Genome|History, 20th Century|Humans|Research', 'Historical Article', '10.1093/bioinformatics/16.1.65', '10812478', 'The development of in silico genomics has progressed slowly in France for a number of political reasons. Two administrative organizations, the Groupement de Recherche sur les Génomes (GREG) and the Groupement de Recherche 1029 (GDR 1029) of the Centre National de la Recherche Scientifique (CNRS) have been established. These organizations have created the dynamics that hopefully will place France (which coordinated consortia that completed several of the first large microbial genomes) among the developed nations that support Large-Scale Biology.'),
(69703, 2000, 'bio', 'Bioinformatics education--a UK perspective', 'Brass, A', 'Regulation of Gene Expression, Institut Pasteur, Paris, France. adanchin@pasteur.fr', 'France', 16, 'Computational Biology|Education, Graduate|Humans|United Kingdom', 'Editorial', '10.1093/bioinformatics/16.2.77', '10842726', '-'),
(69704, 2000, 'bio', 'The complexities of genome analysis, the Retroid agent perspective', 'McClure, M A', 'Department of Microbiology, Montana State University, Bozeman, USA. mars@parvati.msu.montana.edu', 'United States', 0, 'Animals|Badnavirus|Caulimovirus|DNA Transposable Elements|Evolution, Molecular|Genome, Viral|Hepadnaviridae|Humans|RNA|Retroviridae', 'Journal Article', '10.1093/bioinformatics/16.2.79', '10842727', 'The sequences of Retroid agents from a wide diversity of organisms constitute the largest set of complete genomes currently available for the study of genomic architecture and the transfer of information within and between organisms. These agents are ubiquitous in Eukaryotes, comprising 50-90% of the genomic information in some cases.'),
(69705, 2000, 'bio', 'Self-organization and competition in the immune response to cancer invasion: a phase-orientated computational model of oncogenesis', 'Oprixc5x9fan, S A|Ardelean, A|Frangopol, P T', 'Al.I. Cuza University, Department of Theoretical Physics, Iaxc5x9fi, Romania. soprisan@uno.edu|Al.I. Cuza University, Department of Theoretical Physics, Iaxc5x9fi, Romania. soprisan@uno.edu|Al.I. Cuza University, Department of Theoretical Physics, Iaxc5x9fi, Romania. soprisan@uno.edu', 'Romania|Romania|Romania', 6, 'Computer Simulation|Humans|Mathematical Computing|Models, Immunological|Neoplasm Invasiveness', 'Journal Article', '10.1093/bioinformatics/16.2.96', '10842728', 'Recent studies indicate that fractal dimensions can uncover aspects of cellular dynamics prior to pathological manifestation. In this respect we are interested in building a computational model of oncogenesis able to generate patterns with the same fractal dimension spectrum as the in vivo tumor.'),
(69706, 2000, 'bio', 'Darwin v 20: an interpreted computer language for the biosciences', 'Gonnet, G H|Hallett, M T|Korostensky, C|Bernardin, L', 'Department of Computer Science, ETH Zürich, Switzerland.|Department of Computer Science, ETH Zürich, Switzerland.|Department of Computer Science, ETH Zürich, Switzerland.|Department of Computer Science, ETH Zürich, Switzerland.', 'Switzerland|Switzerland|Switzerland|Switzerland', 0, 'Algorithms|Databases, Factual|Mathematical Computing|Peptides|Phylogeny|Programming Languages|Sequence Alignment', 'Journal Article', '10.1093/bioinformatics/16.2.101', '10842729', 'We announce the availability of the second release of Darwin v. 2.0, an interpreted computer language especially tailored to researchers in the biosciences. The system is a general tool applicable to a wide range of problems.'),
(69707, 2000, 'bio', 'Sequence search algorithm assessment and testing toolkit (SAT)', 'Park, J|Holm, L|Chothia, C', 'European Bioinformatics Institute, EMBL Outstation, Cambridge, UK. jong@ebi.ac.uk|European Bioinformatics Institute, EMBL Outstation, Cambridge, UK. jong@ebi.ac.uk|European Bioinformatics Institute, EMBL Outstation, Cambridge, UK. jong@ebi.ac.uk', 'United Kingdom|United Kingdom|United Kingdom', 7, 'Algorithms|Databases, Factual|Proteins', 'Journal Article', '10.1093/bioinformatics/16.2.104', '10842730', 'The Sequence Search Algorithm Assessment and Testing Toolkit (SAT) aims to be a complete package for the comparison of different protein homology search algorithms. The structural classification of proteins can provide us with a clear criterion for judgment in homology detection. There have been several assessments based on structural sequences with classifications but a good deal of similar work is now being repeated with locally developed procedures and programs. The SAT will provide developers with a complete package which will save time and produce more comparable performance assessments for search algorithms. The package is complete in the sense that it provides a non-redundant large sequence resource database, a well-characterized query database of proteins domains, all the parsers and some previous results from PSI-BLAST and a hidden markov model algorithm.'),
(69708, 2000, 'bio', 'ProtEST: protein multiple sequence alignments from expressed sequence tags', 'Cuff, J A|Birney, E|Clamp, M E|Barton, G J', 'European Molecular Biology Laboratory Outstation, European Bioinformatics Institute, Cambridge, UK.|European Molecular Biology Laboratory Outstation, European Bioinformatics Institute, Cambridge, UK.|European Molecular Biology Laboratory Outstation, European Bioinformatics Institute, Cambridge, UK.|European Molecular Biology Laboratory Outstation, European Bioinformatics Institute, Cambridge, UK.', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom', 0, 'Amino Acid Sequence|Expressed Sequence Tags|Molecular Sequence Data|Protein Biosynthesis|Proteins|Sequence Alignment', 'Journal Article', '10.1093/bioinformatics/16.2.111', '10842731', 'An automatic sequence searching method (ProtEST) is described which constructs multiple protein sequence alignments from protein sequences and translated expressed sequence tags (ESTs). ProtEST is more effective than a simple TBLASTN search of the query against the EST database, as the sequences are automatically clustered, assembled, made non-redundant, checked for sequence errors, translated into protein and then aligned and displayed.'),
(69709, 2000, 'bio', 'Fast assignment of protein structures to sequences using the intermediate sequence library PDB-ISL', 'Teichmann, S A|Chothia, C|Church, G M|Park, J', 'MRC Laboratory of Molecular Biology, Cambridge, UK. sat@mrc-lmb.cam.ac.uk|MRC Laboratory of Molecular Biology, Cambridge, UK. sat@mrc-lmb.cam.ac.uk|MRC Laboratory of Molecular Biology, Cambridge, UK. sat@mrc-lmb.cam.ac.uk|MRC Laboratory of Molecular Biology, Cambridge, UK. sat@mrc-lmb.cam.ac.uk', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom', 39, 'Peptide Library|Proteins|Sequence Analysis|Time Factors', 'Journal Article', '10.1093/bioinformatics/16.2.117', '10842732', 'For large-scale structural assignment to sequences, as in computational structural genomics, a fast yet sensitive sequence search procedure is essential. A new approach using intermediate sequences was tested as a shortcut to iterative multiple sequence search methods such as PSI-BLAST.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(69710, 2000, 'bio', 'SAWTED: structure assignment with text description--enhanced detection of remote homologues with automated SWISS-PROT annotation comparisons', 'MacCallum, R M|Kelley, L A|Sternberg, M J', 'Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, UK. R.MacCallum@icrf.icnet.uk|Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, UK. R.MacCallum@icrf.icnet.uk|Biomolecular Modelling Laboratory, Imperial Cancer Research Fund, London, UK. R.MacCallum@icrf.icnet.uk', 'United Kingdom|United Kingdom|United Kingdom', 0, 'Algorithms|Automation|Databases, Factual|Internet|Proteins', 'Comparative Study', '10.1093/bioinformatics/16.2.125', '10842733', 'Sequence database search methods often identify putative sub-threshold hits of known function or structure for a given query sequence. It is widespread practice to filter these hits by hand using knowledge of function and other factors, to the expert, some hits may appear more sensible than others. SAWTED (Structure Assignment With Text Description) is an automated solution to this post-filtering problem which will be applicable to large scale genome assignments.'),
(69711, 2000, 'bio', 'TOPAL 20: improved detection of mosaic sequences within multiple alignments', 'McGuire, G|Wright, F', 'Isaac Newton Institute for Mathematical Sciences, Cambridge, UK.|Isaac Newton Institute for Mathematical Sciences, Cambridge, UK.', 'United Kingdom|United Kingdom', 99, 'Algorithms|Genetic Variation|Mathematical Computing|Recombination, Genetic|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/16.2.130', '10842734', 'The Dss statistic was proposed by McGuire et al. (Mol. Biol. Evol., 14, 1125-1131, 1997) for scanning data sets for the presence of recombination, an important step in some phylogenetic analyses. The statistic, however, could not distinguish well between among-site rate variation and recombination, and had no statistical test for significant values. This paper addresses these shortfalls.'),
(69712, 2000, 'bio', 'TEXshade: shading and labeling of multiple sequence alignments using LATEX2 epsilon', 'Beitz, E', 'Faculty of Chemistry and Pharmacy, University of Tübingen, Germany. eric.beitz@uni-tuebingen.de', 'Germany', 218, 'Algorithms|DNA Fingerprinting|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/16.2.135', '10842735', 'Typesetting, shading and labeling of nucleotide and peptide alignments using standard word processing or graphics software is time consuming. Available automatic sequence shading programs usually do not allow manual application of additional shadings or labels. Hence, a flexible alignment shading package was designed for both calculated and manual shading, using the macro language of the scientific typesetting software LATEX2 epsilon.'),
(69713, 2000, 'bio', 'Single column discrepancy and dynamic max-mini optimizations for quickly finding the most parsimonious evolutionary trees', 'Purdom, P W|Bradford, P G|Tamura, K|Kumar, S', 'Computer Science Department, Indiana University, Bloomington 47405-4101, USA.|Computer Science Department, Indiana University, Bloomington 47405-4101, USA.|Computer Science Department, Indiana University, Bloomington 47405-4101, USA.|Computer Science Department, Indiana University, Bloomington 47405-4101, USA.', 'India|India|India|India', 0, 'Amino Acids|DNA|Evolution, Molecular|Humans|Phylogeny|Time Factors', 'Journal Article', '10.1093/bioinformatics/16.2.140', '10842736', 'In the maximum parsimony (MP) method, the tree requiring the minimum number of changes (discrepancy) to explain the given set of DNA or amino acid sequences is chosen to represent their evolutionary relationships. To find the MP tree, the branch-and-bound algorithm is normally used. For a partial phylogenetic-tree (one that has a subset of the organisms) the traditional algorithm assigns a cost equal to the discrepancy of the partial phylogenetic-tree. We propose a single column discrepancy heuristic which increases this cost by predicting a minimum additional discrepancy needed to attach the sequences yet to be added to the partial phylogenetic-tree. A dynamic Max-mini order of sequence addition is also proposed to quickly terminate branch-and-bound search paths that are guaranteed to lead to suboptimal solutions.'),
(69714, 2000, 'bio', 'Modeling splice sites with Bayes networks', 'Cai, D|Delcher, A|Kao, B|Kasif, S', 'Department of Electrical Engineering and Computer Science, University of Illinois, Chicago 60607, USA.|Department of Electrical Engineering and Computer Science, University of Illinois, Chicago 60607, USA.|Department of Electrical Engineering and Computer Science, University of Illinois, Chicago 60607, USA.|Department of Electrical Engineering and Computer Science, University of Illinois, Chicago 60607, USA.', 'United States|United States|United States|United States', 0, 'Bayes Theorem|Computer Simulation|DNA|Humans|Models, Statistical|Neural Networks (Computer)|RNA Splicing|Software', 'Journal Article', '10.1093/bioinformatics/16.2.152', '10842737', 'The main goal in this paper is to develop accurate probabilistic models for important functional regions in DNA sequences (e.g. splice junctions that signal the beginning and end of transcription in human DNA). These methods can subsequently be utilized to improve the performance of gene-finding systems. The models built here attempt to model long-distance dependencies between non-adjacent bases.'),
(69715, 2000, 'bio', 'STAR/mmCIF: an ontology for macromolecular structure', 'Westbrook, J D|Bourne, P E', 'Rutgers, State University of New Jersey, Department of Chemistry, Piscataway 08854-8087, USA. jwest@rcsb.rutgers.edu|Rutgers, State University of New Jersey, Department of Chemistry, Piscataway 08854-8087, USA. jwest@rcsb.rutgers.edu', 'Jersey|Jersey', 0, 'Crystallography, X-Ray|Databases, Factual|Humans|Information Storage and Retrieval|Macromolecular Substances|Molecular Structure|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/16.2.159', '10842738', 'Crystallographers were motivated 10 years ago to develop a simple and consistent data representation for the exchange and archiving of data associated with the crystallographic experiment and the final structure. As this process evolved (and the data grew at near exponential rates) came the recognition that this representation should also facilitate the automated management of the data and, with the aid of additional software for verification and validation, provide improved consistency and accuracy and hence improved scientific inquiry. This realization led to a new Dictionary Definition Language (DDL) and an extensive dictionary based on this DDL for describing macromolecular structure. In broad terms this could be considered an ontology. An important feature in the development of the ontology was the endorsement and ongoing maintenance and support of the International Union of Crystallography (IUCr). While the description of macromolecular structure and the x-ray crystallographic experiment used to derive it represent explicit data, the ontology is extensible and applicable to other less well-characterized data domains.'),
(69716, 2000, 'bio', 'PNAD-CSS: a workbench for constructing a protein name abbreviation dictionary', 'Yoshida, M|Fukuda, K|Takagi, T', 'Human Genome Center, University of Tokyo, Japan. mikio@ims.u-tokyo.ac.jp|Human Genome Center, University of Tokyo, Japan. mikio@ims.u-tokyo.ac.jp|Human Genome Center, University of Tokyo, Japan. mikio@ims.u-tokyo.ac.jp', 'Japan|Japan|Japan', 0, 'Databases, Factual|Humans|Information Storage and Retrieval|Internet|Proteins', 'Journal Article', '10.1093/bioinformatics/16.2.169', '10842739', 'Since their initial development, integration and construction of databases for molecular-level data have progressed. Though biological molecules are related to each other and form a complex system, the information is stored in the vast archives of the literature or in diverse databases. There is no unified naming convention for biological object, and biological terms may be ambiguous or polysemic. This makes the integration and interaction of databases difficult. In order to eliminate these problems, machine-readable natural language resources appear to be quite promising. We have developed a workbench for protein name abbreviation dictionary (PNAD) building.'),
(69717, 2000, 'bio', 'The human transcript database: a catalogue of full length cDNA inserts', 'Bouck, J|McLeod, M P|Worley, K|Gibbs, R A', 'Baylor College of Medicine, Houston, TX 77030, USA. jbouck@bcm.tmc.edu|Baylor College of Medicine, Houston, TX 77030, USA. jbouck@bcm.tmc.edu|Baylor College of Medicine, Houston, TX 77030, USA. jbouck@bcm.tmc.edu|Baylor College of Medicine, Houston, TX 77030, USA. jbouck@bcm.tmc.edu', 'United States|United States|United States|United States', 4, 'DNA Transposable Elements|DNA, Complementary|Databases, Factual|Humans|RNA, Messenger', 'Journal Article', '10.1093/bioinformatics/16.2.176', '10842740', 'Full length cDNA sequences are an important resource for the research community but are currently intermingled with other sequences. We have identified the human full length insert cDNA sequences in GenBank and placed them in a single location, the Human Transcript Database. AVAILIBILITY: The Human Transcript Database is available at http://www.hgsc.bcm.tms.edu/HTDB/.'),
(69718, 2000, 'bio', 'Dotlet: diagonal plots in a web browser', 'Junier, T|Pagni, M', 'Swiss Institute of Bioinformatics, Swiss Institute for Experimental Cancer Research, Epalinges, Switzerland. Thomas.Junier@isrec.unil.ch|Swiss Institute of Bioinformatics, Swiss Institute for Experimental Cancer Research, Epalinges, Switzerland. Thomas.Junier@isrec.unil.ch', 'Switzerland|Switzerland', 0, 'DNA|Internet|Proteins|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/16.2.178', '10842741', 'Dotlet is a program for comparing sequences by the diagonal plot method. It is designed to be platform-independent and to run in a Web browser, thus enabling the majority of researchers to use it.'),
(69719, 2000, 'bio', 'SISEQ: manipulation of multiple sequence and large database files for common platforms', 'Sato, N', 'Department of Biochemistry and Molecular Biology, Faculty of Science, Saitama University, Japan. naokisat@molbiol.saitama-u.ac.jp', 'Japan', 27, 'DNA|Databases, Factual|Information Storage and Retrieval|Software', 'Journal Article', '10.1093/bioinformatics/16.2.180', '10842742', 'A multiple sequence file converter for common platforms, SISEQ,is described, which performs extraction of DNA sequences that correspond to CDS or RNA field of a large database file as well as subsequent multi-sequence conversions for phylogenetic or molecular biological analysis. Command-line interface as well as a GUI and a script-driven operation mode are provided.'),
(69720, 2000, 'bio', 'GOLD--graphical overview of linkage disequilibrium', 'Abecasis, G R|Cookson, W O', 'Wellcome Trust Centre for Human Genetics, University of Oxford, UK. goncalo@well.ox.ac.uk|Wellcome Trust Centre for Human Genetics, University of Oxford, UK. goncalo@well.ox.ac.uk', 'United Kingdom|United Kingdom', 0, 'Computer Graphics|Haplotypes|Humans|Linkage Disequilibrium|Software', 'Journal Article', '10.1093/bioinformatics/16.2.182', '10842743', 'We describe a software package that provides a graphical summary of linkage disequilibrium in human genetic data. It allows for the analysis of family data and is well suited to the analysis of dense genetic maps.'),
(69721, 2000, 'bio', 'TAMBIS: transparent access to multiple bioinformatics information sources', 'Stevens, R|Baker, P|Bechhofer, S|Ng, G|Jacoby, A|Paton, N W|Goble, C A|Brass, A', 'Department of Computer Science and School of Biological Sciences, University of Manchester, UK.|Department of Computer Science and School of Biological Sciences, University of Manchester, UK.|Department of Computer Science and School of Biological Sciences, University of Manchester, UK.|Department of Computer Science and School of Biological Sciences, University of Manchester, UK.|Department of Computer Science and School of Biological Sciences, University of Manchester, UK.|Department of Computer Science and School of Biological Sciences, University of Manchester, UK.|Department of Computer Science and School of Biological Sciences, University of Manchester, UK.|Department of Computer Science and School of Biological Sciences, University of Manchester, UK.', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom', 213, 'Computational Biology|Information Storage and Retrieval|Software', 'Journal Article', '10.1093/bioinformatics/16.2.184', '10842744', 'TAMBIS (Transparent Access to Multiple Bioinformatics Information Sources) is an application that allows biologists to ask rich and complex questions over a range of bioinformatics resources. It is based on a model of the knowledge of the concepts and their relationships in molecular biology and bioinformatics.'),
(69722, 2000, 'bio', 'Two or three myths about bioinformatics', 'Ouzounis, C', 'Department of Computer Science and School of Biological Sciences, University of Manchester, UK.', 'United Kingdom', 8, 'Computational Biology', 'Editorial', '10.1093/bioinformatics/16.3.187', '10869011', '-'),
(69723, 2000, 'bio', 'Homology-based gene structure prediction: simplified matching algorithm using a translated codon (tron) and improved accuracy by allowing for long gaps', 'Gotoh, O', 'Saitama Cancer Center Research Institute, 818 Komuro Ina-machi, Saitama 362-0806, Japan. gotoh@cancer-c.pref.saitama.jp', 'Japan', 0, 'Algorithms|Amino Acid Sequence|Animals|Caenorhabditis elegans|Codon|Genes, Helminth|Molecular Sequence Data|Protein Biosynthesis|Reproducibility of Results|Sequence Homology, Amino Acid', 'Journal Article', '10.1093/bioinformatics/16.3.190', '10869012', 'Locating protein-coding exons (CDSs) on a eukaryotic genomic DNA sequence is the initial and an essential step in predicting the functions of the genes embedded in that part of the genome. Accurate prediction of CDSs may be achieved by directly matching the DNA sequence with a known protein sequence or profile of a homologous family member(s).'),
(69724, 2000, 'bio', 'Optimal spliced alignment of homologous cDNA to a genomic DNA template', 'Usuka, J|Zhu, W|Brendel, V', 'Department of Chemistry, Stanford University, Stanford, CA 94305, USA Department of Zoology and Genetics, Iowa State University, 2112 Molecular Biology Building, Ames, IA 50011-3260, USA.|Department of Chemistry, Stanford University, Stanford, CA 94305, USA Department of Zoology and Genetics, Iowa State University, 2112 Molecular Biology Building, Ames, IA 50011-3260, USA.|Department of Chemistry, Stanford University, Stanford, CA 94305, USA Department of Zoology and Genetics, Iowa State University, 2112 Molecular Biology Building, Ames, IA 50011-3260, USA.', 'United States|United States|United States', 107, 'Algorithms|Arabidopsis|Base Sequence|DNA, Complementary|Molecular Sequence Data|RNA Splicing|Sequence Alignment|Sequence Homology, Nucleic Acid|Templates, Genetic', 'Journal Article', '10.1093/bioinformatics/16.3.203', '10869013', 'Supplementary cDNA or EST evidence is often decisive for discriminating between alternative gene predictions derived from computational sequence inspection by any of a number of requisite programs. Without additional experimental effort, this approach must rely on the occurrence of cognate ESTs for the gene under consideration in available, generally incomplete, EST collections for the given species. In some cases, particular exon assignments can be supported by sequence matching even if the cDNA or EST is produced from non-cognate genomic DNA, including different loci of a gene family or homologous loci from different species. However, marginally significant sequence matching alone can also be misleading. We sought to develop an algorithm that would simultaneously score for predicted intrinsic splice site strength and sequence matching between the genomic DNA template and a related cDNA or EST. In this case, weakly predicted splice sites may be chosen for the optimal scoring spliced alignment on the basis of surrounding sequence matching. Strongly predicted splice sites will enter the optimal spliced alignment even without strong sequence matching.'),
(69725, 2000, 'bio', 'Net nearest neighbor analysis (NNNA) summarizes non-compensated dinucleotides within gene sequences', 'Lang, D M', 'Department of Computer Science, University of Abertay-Dundee, Bell Street, Dundee, DD1 1HG, UK.', 'United Kingdom', 0, 'Dinucleotide Repeats|Escherichia coli|Humans|Insulin|Nucleotides|Phylogeny|Proinsulin|Protein Precursors|RNA, Bacterial|RNA, Transfer|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/16.3.212', '10869014', 'Net Nearest Neighbor Analysis (NNNA) measures a previously unexamined aspect of dinucleotide frequency-the non-compensated, non-repetitive dinucleotides in a sequence. Non-compensated dinucleotides are those in excess of their corresponding reverse dinucleotides.'),
(69726, 2000, 'bio', 'Combinatorial motif analysis and hypothesis generation on a genomic scale', 'Hu, Y J|Sandmeyer, S|McLaughlin, C|Kibler, D', 'Information and Computer Science Department, Department of Biological Chemistry, College of Medicine, University of California, Irvine, USA.|Information and Computer Science Department, Department of Biological Chemistry, College of Medicine, University of California, Irvine, USA.|Information and Computer Science Department, Department of Biological Chemistry, College of Medicine, University of California, Irvine, USA.|Information and Computer Science Department, Department of Biological Chemistry, College of Medicine, University of California, Irvine, USA.', 'United States|United States|United States|United States', 21, 'Algorithms|Genes, Fungal|Regulatory Sequences, Nucleic Acid|Regulon|Saccharomyces cerevisiae', 'Journal Article', '10.1093/bioinformatics/16.3.222', '10869015', 'Computer-assisted methods are essential for the analysis of biosequences. Gene activity is regulated in part by the binding of regulatory molecules (transcription factors) to combinations of short motifs. The goal of our analysis is the development of algorithms to identify regulatory motifs and to predict the activity of combinations of those motifs.'),
(69727, 2000, 'bio', 'Fast probabilistic analysis of sequence function using scoring matrices', 'Wu, T D|Nevill-Manning, C G|Brutlag, D L', 'Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA. twu@gene.com|Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA. twu@gene.com|Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA. twu@gene.com', 'United States|United States|United States', 0, 'Markov Chains|Probability|Sequence Analysis|Software|Time Factors', 'Journal Article', '10.1093/bioinformatics/16.3.233', '10869016', 'We present techniques for increasing the speed of sequence analysis using scoring matrices. Our techniques are based on calculating, for a given scoring matrix, the quantile function, which assigns a probability, or p, value to each segmental score. Our techniques also permit the user to specify a p threshold to indicate the desired trade-off between sensitivity and speed for a particular sequence analysis. The resulting increase in speed should allow scoring matrices to be used more widely in large-scale sequencing and annotation projects.'),
(69728, 2000, 'bio', 'Adaptive encoding neural networks for the recognition of human signal peptide cleavage sites', 'Jagla, B|Schuchhardt, J', 'Freie Universität Berlin, Institut für Med./Techn. Physik und Lasermedizin, Krahmerstrasse 6-10, 12045 Berlin, Germany.|Freie Universität Berlin, Institut für Med./Techn. Physik und Lasermedizin, Krahmerstrasse 6-10, 12045 Berlin, Germany.', 'Germany|Germany', 0, 'Binding Sites|Humans|Neural Networks (Computer)|Protein Sorting Signals|Proteins', 'Journal Article', '10.1093/bioinformatics/16.3.245', '10869017', 'Data representation and encoding are essential for classification of protein sequences with artificial neural networks (ANN). Biophysical properties are appropriate for low dimensional encoding of protein sequence data. However, in general there is no a priori knowledge of the relevant properties for extraction of representative features.'),
(69729, 2000, 'bio', 'Predicting the oxidation state of cysteines by multiple sequence alignment', 'Fiser, A|Simon, I', 'Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest H-1518, PO Box 7, Hungary. fisera@rockefeller.edu|Institute of Enzymology, Biological Research Center, Hungarian Academy of Sciences, Budapest H-1518, PO Box 7, Hungary. fisera@rockefeller.edu', 'Hungary|Hungary', 77, 'Conserved Sequence|Cysteine|Cystine|Oxidation-Reduction|Predictive Value of Tests|Protein Processing, Post-Translational|Sequence Alignment', 'Journal Article', '10.1093/bioinformatics/16.3.251', '10869018', 'Protein sequences found in databanks usually do not report post translational covalent modifications such as the oxidation state of cystein (Cys) residues. Accurate prediction of whether a functionally or structurally important Cys occurs in the oxidized or thiol form would be helpful for molecular biology experiments and structure prediction.'),
(69730, 2000, 'bio', 'Sequence-structure specificity of a knowledge based energy function at the secondary structure level', 'Xu, D|Unseren, M A|Xu, Y|Uberbacher, E C', 'Computational Biosciences Section, Life Sciences Division Center for Engineering Science Advanced Research, Computer Science and Mathematics Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6480, USA. xud@ornl.gov|Computational Biosciences Section, Life Sciences Division Center for Engineering Science Advanced Research, Computer Science and Mathematics Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6480, USA. xud@ornl.gov|Computational Biosciences Section, Life Sciences Division Center for Engineering Science Advanced Research, Computer Science and Mathematics Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6480, USA. xud@ornl.gov|Computational Biosciences Section, Life Sciences Division Center for Engineering Science Advanced Research, Computer Science and Mathematics Division, Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6480, USA. xud@ornl.gov', 'United States|United States|United States|United States', 0, 'Amino Acid Sequence|Databases, Factual|Energy Transfer|Molecular Sequence Data|Protein Structure, Secondary|Proteins|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/16.3.257', '10869019', 'This paper investigates the sequence-structure specificity of a representative knowledge based energy function by applying it to threading at the level of secondary structures of proteins. Assessing the strengths and weaknesses of an energy function at this fundamental level provides more detailed and insightful information than at the tertiary structure level and the results obtained can be useful in tertiary level threading.'),
(69731, 2000, 'bio', 'An ontology for biological function based on molecular interactions', 'Karp, P D', 'Bioinformatics Research Group, SRI International, EK223, 333 Ravenswood Avenue, Menlo Park, CA 94025, USA. pkarp@ai.sri.com', 'United States', 122, 'Computational Biology|Computing Methodologies|Databases, Factual|Proteins', 'Journal Article', '10.1093/bioinformatics/16.3.269', '10869020', 'A number of important bioinformatics computations involve computing with function: executing computational operations whose inputs or outputs are descriptions of the functions of biomolecules. Examples include performing functional queries to sequence and pathway databases, and determining functional equality to evaluate algorithms that predict function from sequence. A prerequisite to computing with function is the existence of an ontology that provides a structured semantic encoding of function. Functional bioinformatics is an emerging subfield of bioinformatics that is concerned with developing ontologies and algorithms for computing with biological function.'),
(69732, 2000, 'bio', 'MPSA: integrated system for multiple protein sequence analysis with client/server capabilities', 'Blanchet, C|Combet, C|Geourjon, C|Deléage, G', 'Institut de Biologie et Chimie des Protéines, BCP-CNRS UPR 412, Laboratoire de conformation des Protéines, 7, Passage du Vercors, 69 367, Lyon Cedex 07, France. c.blanchet@ibcp.fr|Institut de Biologie et Chimie des Protéines, BCP-CNRS UPR 412, Laboratoire de conformation des Protéines, 7, Passage du Vercors, 69 367, Lyon Cedex 07, France. c.blanchet@ibcp.fr|Institut de Biologie et Chimie des Protéines, BCP-CNRS UPR 412, Laboratoire de conformation des Protéines, 7, Passage du Vercors, 69 367, Lyon Cedex 07, France. c.blanchet@ibcp.fr|Institut de Biologie et Chimie des Protéines, BCP-CNRS UPR 412, Laboratoire de conformation des Protéines, 7, Passage du Vercors, 69 367, Lyon Cedex 07, France. c.blanchet@ibcp.fr', 'France|France|France|France', 23, 'Computing Methodologies|Internet|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/16.3.286', '10869021', 'MPSA is a stand-alone software intended to protein sequence analysis with a high integration level and Web clients/server capabilities. It provides many methods and tools, which are integrated into an interactive graphical user interface. It is available for most Unix/Linux and non-Unix systems. MPSA is able to connect to a Web server (e.g. http://pbil.ibcp.fr/NPSA) in order to perform large-scale sequence comparison on up-to-date databanks.'),
(69733, 2000, 'bio', 'Storing biological sequence databases in relational form', 'Xie, G|DeMarco, R|Blevins, R|Wang, Y', 'Department of Bioinformatics, Merck & Co., Inc., WP42-300, West Point, PA 19486, USA.|Department of Bioinformatics, Merck & Co., Inc., WP42-300, West Point, PA 19486, USA.|Department of Bioinformatics, Merck & Co., Inc., WP42-300, West Point, PA 19486, USA.|Department of Bioinformatics, Merck & Co., Inc., WP42-300, West Point, PA 19486, USA.', 'United States|United States|United States|United States', 11, 'Amino Acid Sequence|Base Sequence|Computational Biology|Databases, Factual|Software', 'Journal Article', '10.1093/bioinformatics/16.3.288', '10869022', 'We have created a set of applications using Perl and Java in combination with XML technology to install biological sequence databases into an Oracle RDBMS. An easy-to-use interface using Java has been created for database query and other tools developed to integrate with our in-house bioinformatics applications. AVAILIBILITY: The database schema, DTD file, and source codes are available from the authors via email.'),
(69734, 2000, 'bio', 'PIR: a new resource for bioinformatics', 'McGarvey, P B|Huang, H|Barker, W C|Orcutt, B C|Garavelli, J S|Srinivasarao, G Y|Yeh, L S|Xiao, C|Wu, C H', 'Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road, NW, Washington, DC 20007, USA.|Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road, NW, Washington, DC 20007, USA.|Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road, NW, Washington, DC 20007, USA.|Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road, NW, Washington, DC 20007, USA.|Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road, NW, Washington, DC 20007, USA.|Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road, NW, Washington, DC 20007, USA.|Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road, NW, Washington, DC 20007, USA.|Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road, NW, Washington, DC 20007, USA.|Protein Information Resource, National Biomedical Research Foundation, 3900 Reservoir Road, NW, Washington, DC 20007, USA.', 'United States|United States|United States|United States|United States|United States|United States|United States|United States', 29, 'Animals|Caenorhabditis elegans|Computational Biology|Databases, Factual|Helminth Proteins|Humans|Internet|Phosphotransferases (Alcohol Group Acceptor)|Sulfate Adenylyltransferase', 'Journal Article', '10.1093/bioinformatics/16.3.290', '10869023', 'The Protein Information Resource (PIR) has greatly expanded its Web site and developed a set of interactive search and analysis tools to facilitate the analysis, annotation, and functional identification of proteins. New search engines have been implemented to combine sequence similarity search results with database annotation information. The new PIR search systems have proved very useful in providing enriched functional annotation of protein sequences, determining protein superfamily-domain relationships, and detecting annotation errors in genomic database archives.'),
(69735, 2000, 'bio', 'HELM: searching for helix motifs within protein sequences', 'Facchiano, A M', 'CRISCEB, Centro di Ricerca Interdipartimentale di Scienze Computazionali e Biotecnologiche, Seconda Universitàdi Napoli - via Costantinopoli 16, 80138 Napoli, Italy. angelo@crisceb.area.na.cnr.it', 'Italy', 0, 'Amino Acid Motifs|Internet|Plant Proteins|Proteins|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/16.3.292', '10869024', 'HELM is a web tool designed to automate the analysis of protein sequences searching for alpha helix motifs. This analysis can be useful in protein engineering studies, aimed at the identification of regions to be modified in order to obtain more suitable features of local and/or global stability.'),
(69736, 2000, 'bio', 'EDIBLE: experimental design and information calculations in phylogenetics', 'Massingham, T|Goldman, N', 'Department of Genetics, Downing Street, Cambridge CB2 3EH, UK.|Department of Genetics, Downing Street, Cambridge CB2 3EH, UK.', 'United Kingdom|United Kingdom', 0, 'Likelihood Functions|Markov Chains|Phylogeny|Software', 'Journal Article', '10.1093/bioinformatics/16.3.294', '10869025', 'Although evolutionary inference from molecular sequences is a statistical problem, little attention has been paid to questions of experimental design. A computer program, EDIBLE, has been developed to perform likelihood calculations based on Markov process models of nucleotide substitution allied with phylogenetic trees, and from these to compute Fisher information measures under different experimental designs. These calculations can be used to answer questions of optimal experimental design in molecular phylogenetics.'),
(69737, 2000, 'bio', 'RRTree: relative-rate tests between groups of sequences on a phylogenetic tree', 'Robinson-Rechavi, M|Huchon, D', 'Department of Zoology, Tel Aviv University, Ramat Aviv 69978, Israel Institut des Sciences de lEvolution, UniversitéMontpellier 2, 34095 Montpellier, France. mark.robinson@ens-lyon.fr|Department of Zoology, Tel Aviv University, Ramat Aviv 69978, Israel Institut des Sciences de lEvolution, UniversitéMontpellier 2, 34095 Montpellier, France. mark.robinson@ens-lyon.fr', 'France|France', 303, 'Algorithms|DNA|Phylogeny|Proteins|Sequence Analysis|Software', 'Journal Article', '10.1093/bioinformatics/16.3.296', '10869026', 'RRTree is a user-friendly program for comparing substitution rates between lineages of protein or DNA sequences, relative to an outgroup, through relative rate tests. Genetic diversity is taken into account through use of several sequences, and phylogenetic relations are integrated by topological weighting.'),
(69738, 2000, 'bio', 'PRoMT: inferring demographic history from DNA sequences', 'Wooding, S', 'Department of Anthropology, University of Utah, 270 South 1400 East, Salt Lake City, UT 84112-0060, USA. stephen.wooding@anthro.utah.edu', 'United States', 0, 'Algorithms|Base Sequence|DNA|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/16.3.298', '10869027', 'I describe a parallel implementation of Rogers mismatch algorithm, a method for making inferences about demographic history from DNA sequence data. The program is distributed on clusters of workstations, providing a substantial speedup and low execution times on large numbers of nodes.'),
(69739, 2000, 'bio', 'GABAagent: a system for integrating data on GABA receptors', 'Rachedi, A|Rebhan, M|Xue, H', 'Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.|Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.|Department of Biochemistry, Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong.', 'Hong Kong|Hong Kong|Hong Kong', 0, 'Databases, Factual|Humans|Internet|Receptors, GABA', 'Journal Article', '10.1093/bioinformatics/16.4.301', '10869028', 'Scientific data pertaining to GABA receptors, which are of medical importance, are widely scattered throughout numerous heterogeneous Internet resources. This situation has made the integrated acquisition of such data difficult and substantially time consuming even for researchers who are Internet aficionados. Thus, there exists a genuine need for the development of Internet applications, such as GABAagent, which provide efficient and timely access to concise and integrated information.'),
(69740, 2000, 'bio', 'JESAM: CORBA software components to create and publish EST alignments and clusters', 'Parsons, J D|Rodriguez-Tomé, P', 'EMBL-Outstation, The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. jparsons@ebi.ac.uk|EMBL-Outstation, The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. jparsons@ebi.ac.uk', 'United Kingdom|United Kingdom', 5, 'Animals|Databases, Factual|Expressed Sequence Tags|Humans|Mice|Rats|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/16.4.313', '10869029', 'Expressed Sequence Tags (ESTs) are cheap, easy and quick to obtain relative to full genomic sequencing and currently sample more eukaryotic genes than any other data source. They are particularly useful for developing Sequence Tag Sites (STSs for mapping), polymorphism discovery, disease gene hunting, mass spectrometer proteomics, and most ironically for finding genes and predicting gene structure after the great effort of genomic sequencing. However, ESTs have many problems and the public EST databases contain all the errors and high redundancy intrinsic to the submitted data so it is often found that derived database views, which reduce both errors and redundancy, are more effective starting points for research than the original raw submissions. Existing derived views such as EST cluster databases and consensus databases have never published supporting evidence or intermediary results leading to difficulties trusting, correcting, and customizing the final published database. These difficulties have lead many groups to wastefully repeat the complex intermediary work of others in order to offer slightly different final views. A better approach might be to discover the most expensive common calculations used by all the approaches and then publish all intermediary results. Given a globally accessible database with a suitable component interface, like the JESAM software described in this paper, the creation of customized EST-derived databases could be achieved with minimum effort.'),
(69741, 2000, 'bio', 'Automatic discovery of regulatory patterns in promoter regions based on whole cell expression data and functional annotation', 'Jensen, L J|Knudsen, S', 'Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark.|Center for Biological Sequence Analysis, Department of Biotechnology, Building 208, The Technical University of Denmark, DK-2800 Lyngby, Denmark.', 'Denmark|Denmark', 81, 'Algorithms|Automation|Binding Sites|Cysteine Endopeptidases|Gene Expression Profiling|Multienzyme Complexes|Promoter Regions, Genetic|Proteasome Endopeptidase Complex|Saccharomyces cerevisiae|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/16.4.326', '10869030', 'The whole genomes submitted to GenBank contain valuable information about the function of genes as well as the upstream sequences and whole cell expression provides valuable information on gene regulation. To utilize these large amounts of data for a biological understanding of the regulation of gene expression, new automatic methods for pattern finding are needed.'),
(69742, 2000, 'bio', 'The language of RNA: a formal grammar that includes pseudoknots', 'Rivas, E|Eddy, S R', 'Department of Genetics, Washington University, St. Louis, MO 63110, USA.|Department of Genetics, Washington University, St. Louis, MO 63110, USA.', 'United States|United States', 0, 'Algorithms|Nucleic Acid Conformation|RNA', 'Journal Article', '10.1093/bioinformatics/16.4.334', '10869031', 'In a previous paper, we presented a polynomial time dynamic programming algorithm for predicting optimal RNA secondary structure including pseudoknots. However, a formal grammatical representation for RNA secondary structure with pseudoknots was still lacking.'),
(69743, 2000, 'bio', 'SPLASH: structural pattern localization analysis by sequential histograms', 'Califano, A', 'IBM TJ Watson Research Center, PO Box 704, Yorktown Heights, NY 10598, USA. acal@us.ibm.com', 'United States', 0, 'Algorithms|Amino Acids|Animals|Chickens|DNA|Databases, Factual|Histones|Proteins|Receptors, Cell Surface|Sequence Analysis, DNA|Sequence Analysis, Protein', 'Journal Article', '10.1093/bioinformatics/16.4.341', '10869032', 'The discovery of sparse amino acid patterns that match repeatedly in a set of protein sequences is an important problem in computational biology. Statistically significant patterns, that is patterns that occur more frequently than expected, may identify regions that have been preserved by evolution and which may therefore play a key functional or structural role. Sparseness can be important because a handful of non-contiguous residues may play a key role, while others, in between, may be changed without significant loss of function or structure. Similar arguments may be applied to conserved DNA patterns. Available sparse pattern discovery algorithms are either inefficient or impose limitations on the type of patterns that can be discovered.'),
(69744, 2000, 'bio', 'PROF_ PAT 13: updated database of patterns used to detect local similarities', 'Bachinsky, A G|Frolov, A S|Naumochkin, A N|Nizolenko, L P|Yarigin, A A', 'Theoretical Department, Research Institute of Molecular Biology, SRC VB Vector, Koltsovo, Novosibirsk region, 630559, Russia. bachin@vector.nsc.ru|Theoretical Department, Research Institute of Molecular Biology, SRC VB Vector, Koltsovo, Novosibirsk region, 630559, Russia. bachin@vector.nsc.ru|Theoretical Department, Research Institute of Molecular Biology, SRC VB Vector, Koltsovo, Novosibirsk region, 630559, Russia. bachin@vector.nsc.ru|Theoretical Department, Research Institute of Molecular Biology, SRC VB Vector, Koltsovo, Novosibirsk region, 630559, Russia. bachin@vector.nsc.ru|Theoretical Department, Research Institute of Molecular Biology, SRC VB Vector, Koltsovo, Novosibirsk region, 630559, Russia. bachin@vector.nsc.ru', '-|-|-|-|-', 11, 'Databases, Factual|Proteins|Sequence Analysis, Protein|Sequence Homology, Amino Acid', 'Journal Article', '10.1093/bioinformatics/16.4.358', '10869033', 'When analysing novel protein sequences, it is now essential to extend search strategies to include a range of secondary databases. Pattern databases have become vital tools for identifying distant relationships in sequences, and hence for predicting protein function and structure. The main drawback of such methods is the relatively small representation of proteins in trial samples at the time of their construction. Therefore, a negative result of an amino acid sequence comparison with such a databank forces a researcher to search for similarities in the original protein banks. We developed a database of patterns constructed for groups of related proteins with maximum representation of amino acid sequences of SWISS-PROT in the groups.'),
(69745, 2000, 'bio', 'On the convergence of a clustering algorithm for protein-coding regions in microbial genomes', 'Baldi, P', 'Department of Information and Computer Science, University of California, Irvine, CA 92697-3425, USA. pfbaldi@ics.uci.edu', 'United States', 16, 'Algorithms|Computer Simulation|Markov Chains|Proteins', 'Journal Article', '10.1093/bioinformatics/16.4.367', '10869034', 'As the number of fully sequenced prokaryotic genomes continues to grow rapidly, computational methods for reliably detecting protein-coding regions become even more important. Audic and Claverie (1998) Proc. Natl Acad. Sci. USA, 95, 10026-10031, have proposed a clustering algorithm for protein-coding regions in microbial genomes. The algorithm is based on three Markov models of order k associated with subsequences extracted from a given genome. The parameters of the three Markov models are recursively updated by the algorithm which, in simulations, always appear to converge to a unique stable partition of the genome. The partition corresponds to three kinds of regions: (1) coding on the direct strand, (2) coding on the complementary strand, (3) non-coding.'),
(69746, 2000, 'bio', 'Database of structural motifs in proteins', 'Guruprasad, K|Prasad, M S|Kumar, G R', 'Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad - 500 076, India. guru@www.cdfd.org.in|Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad - 500 076, India. guru@www.cdfd.org.in|Centre for DNA Fingerprinting and Diagnostics (CDFD), Nacharam, Hyderabad - 500 076, India. guru@www.cdfd.org.in', 'India|India|India', 0, 'Amino Acid Motifs|Databases, Factual|Proteins', 'Journal Article', '10.1093/bioinformatics/16.4.372', '10869035', 'The database of structural motifs in proteins (DSMP) contains data relevant to helices, beta-turns, gamma-turns, beta-hairpins, psi-loops, beta-alpha-beta motifs, beta-sheets, beta-strands and disulphide bridges extracted from all proteins in the Protein Data Bank primarily using the PROMOTIF program and implemented as a web-based network service using the SRS. The data corresponding to the structural motifs includes, sequence, position in polypeptide chain, geometry, type, unique code, keywords and resolution of crystal structure. This data is available for a representative data set of 1028 protein chains and also for all 10 213 proteins in the Protein Data Bank. The three-dimensional coordinates for all structural motifs (except sheet and disulphide bridge) are also available for the representative data set. Using features in SRS, DSMP can be queried to extract information from one or more structural motifs that may be useful for sequence-structure analysis, prediction, modelling or design.'),
(69747, 2000, 'bio', 'Wavelet change-point prediction of transmembrane proteins', 'Lio, P|Vannucci, M', 'Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK. plio@hgmp.mrc.ac.uk|Department of Genetics, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK. plio@hgmp.mrc.ac.uk', 'United Kingdom|United Kingdom', 73, 'Bacterial Proteins|Humans|Membrane Proteins|Receptors, CCR5', 'Journal Article', '10.1093/bioinformatics/16.4.376', '10869036', 'A non-parametric method, based on a wavelet data-dependent threshold technique for change-point analysis, is applied to predict location and topology of helices in transmembrane proteins. A new propensity scale generated from a transmembrane helix database is proposed.'),
(69748, 2000, 'bio', 'TrExML: a maximum-likelihood approach for extensive tree-space exploration', 'Wolf, M J|Easteal, S|Kahn, M|McKay, B D|Jermiin, L S', 'Department of Mathematics and Computer Science, Bemidji State University, Bemidji, MN 56601-2699, USA. mjwolf@whitetail.bemidji.msus.edu|Department of Mathematics and Computer Science, Bemidji State University, Bemidji, MN 56601-2699, USA. mjwolf@whitetail.bemidji.msus.edu|Department of Mathematics and Computer Science, Bemidji State University, Bemidji, MN 56601-2699, USA. mjwolf@whitetail.bemidji.msus.edu|Department of Mathematics and Computer Science, Bemidji State University, Bemidji, MN 56601-2699, USA. mjwolf@whitetail.bemidji.msus.edu|Department of Mathematics and Computer Science, Bemidji State University, Bemidji, MN 56601-2699, USA. mjwolf@whitetail.bemidji.msus.edu', 'United States|United States|United States|United States|United States', 28, 'Algorithms|Amino Acids|Likelihood Functions|Nucleic Acids|Phylogeny|Sequence Analysis, DNA|Sequence Analysis, Protein', 'Journal Article', '10.1093/bioinformatics/16.4.383', '10869037', 'Maximum-likelihood analysis of nucleotide and amino acid sequences is a powerful approach for inferring phylogenetic relationships and for comparing evolutionary hypotheses. Because it is a computationally demanding and time-consuming process, most algorithms explore only a minute portion of tree-space, with the emphasis on finding the most likely tree while ignoring the less likely, but not significantly worse, trees. However, when such trees exist, it is equally important to identify them to give due consideration to the phylogenetic uncertainty. Consequently, it is necessary to change the focus of these algorithms such that near optimal trees are also identified.'),
(69749, 2000, 'bio', 'Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies', 'Rambaut, A', 'Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK. andrew.rambaut@zoo.ox.ac.uk', 'United Kingdom', 282, 'DNA, Viral|Dengue Virus|Evolution, Molecular|Humans|Likelihood Functions|Phylogeny|Sequence Analysis, DNA|Software|Viral Envelope Proteins', 'Journal Article', '10.1093/bioinformatics/16.4.395', '10869038', 'TipDate is a program that will use sequences that have been isolated at different dates to estimate their rate of molecular evolution. The program provides a maximum likelihood estimate of the rate and also the associated date of the most recent common ancestor of the sequences, under a model which assumes a constant rate of substitution (molecular clock) but which accommodates the dates of isolation. Confidence intervals for these parameters are also estimated.'),
(69750, 2000, 'bio', 'Detecting hypermutations in viral sequences with an emphasis on G --> A hypermutation', 'Rose, P P|Korber, B T', 'Theoretical Biology and Biophysics, Los Alamos National Laboratories, MS K710 Los Alamos, NM 87544, USA. pxr@t10.lanl.gov|Theoretical Biology and Biophysics, Los Alamos National Laboratories, MS K710 Los Alamos, NM 87544, USA. pxr@t10.lanl.gov', 'United States|United States', 207, 'Adenine|Animals|Guanine|Humans|Point Mutation|Software|Viruses', 'Journal Article', '10.1093/bioinformatics/16.4.400', '10869039', 'This program compares sequence sets to a reference sequence, tallies G --> A hypermutations, and presents the results in various tables and graphs, which include dinucleotide context, summaries of all observed nucleotide changes, and stop codons introduced by hypermutation.'),
(69751, 2000, 'bio', 'A browser for expression data', 'Pocock, M R|Hubbard, T J', 'The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. mrp@sanger.ac.uk|The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. mrp@sanger.ac.uk', 'United Kingdom|United Kingdom', 1, 'Databases, Factual|Gene Expression|Software', 'Journal Article', '10.1093/bioinformatics/16.4.402', '10869040', 'We have written a fully extensible Java application for visually browsing expression data, and clusters of genes or experimental conditions calculated from that data. The application requires a run-time environment for Java2.'),
(69752, 2000, 'bio', 'The PSIPRED protein structure prediction server', 'McGuffin, L J|Bryson, K|Jones, D T', 'Protein Bioinformatics Group, Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.|Protein Bioinformatics Group, Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.|Protein Bioinformatics Group, Department of Biological Sciences, University of Warwick, Coventry CV4 7AL, UK.', 'United Kingdom|United Kingdom|United Kingdom', 2352, 'Protein Folding|Protein Structure, Secondary|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/16.4.404', '10869041', 'The PSIPRED protein structure prediction server allows users to submit a protein sequence, perform a prediction of their choice and receive the results of the prediction both textually via e-mail and graphically via the web. The user may select one of three prediction methods to apply to their sequence: PSIPRED, a highly accurate secondary structure prediction method, MEMSAT 2, a new version of a widely used transmembrane topology prediction method, or GenTHREADER, a sequence profile based fold recognition method.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(69753, 2000, 'bio', 'Taxonomic markup language: applying XML to systematic data', 'Gilmour, R', 'Science Library, University at Albany, Albany, NY 12222, USA. gilmr@cnsvax.albany.edu', 'United States', 9, 'Classification|Electronic Data Processing|Phylogeny|Programming Languages', 'Journal Article', '10.1093/bioinformatics/16.4.406', '10869042', 'An XML document type definition (DTD) is provided for the description of taxonomic relationships between organisms. Two XSL style-sheets for the graphical presentation of simple taxonomic trees are also provided.'),
(69754, 2000, 'bio', 'Mathematica packages for simulation of experimental genetics', 'Manly, K F', 'Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA. kmanly@mcbio.med.buffalo.edu', 'United States', 0, 'Animals|Computer Simulation|Mathematical Computing|Models, Genetic|Quantitative Trait, Heritable|Software', 'Journal Article', '10.1093/bioinformatics/16.4.408', '10869043', 'This note describes add-on packages for the Mathematica software system (Wolfram 1996) which allow simulation and analysis of both Mendelian and complex genetic traits in experimental crosses of plants or animals.'),
(69755, 2000, 'bio', 'From data to knowledge', 'Rechenmann, F', 'Molecular and Cellular Biology, Roswell Park Cancer Institute, Buffalo, NY 14263, USA. kmanly@mcbio.med.buffalo.edu', 'United States', 8, 'Artificial Intelligence|Computational Biology|Molecular Biology', 'Editorial', '10.1093/bioinformatics/16.5.411', '10871263', '-'),
(69756, 2000, 'bio', 'Assessing the accuracy of prediction algorithms for classification: an overview', 'Baldi, P|Brunak, S|Chauvin, Y|Andersen, C A|Nielsen, H', 'Department of Information and Computer Science, University of California, Irvine, CA 92697, USA. pfbaldi@ics.uci.edu|Department of Information and Computer Science, University of California, Irvine, CA 92697, USA. pfbaldi@ics.uci.edu|Department of Information and Computer Science, University of California, Irvine, CA 92697, USA. pfbaldi@ics.uci.edu|Department of Information and Computer Science, University of California, Irvine, CA 92697, USA. pfbaldi@ics.uci.edu|Department of Information and Computer Science, University of California, Irvine, CA 92697, USA. pfbaldi@ics.uci.edu', 'United States|United States|United States|United States|United States', 1376, 'Algorithms|Classification|Computational Biology|Learning|Models, Statistical|Neural Networks (Computer)', 'Journal Article', '10.1093/bioinformatics/16.5.412', '10871264', 'We provide a unified overview of methods that currently are widely used to assess the accuracy of prediction algorithms, from raw percentages, quadratic error measures and other distances, and correlation coefficients, and to information theoretic measures such as relative entropy and mutual information. We briefly discuss the advantages and disadvantages of each approach. For classification tasks, we derive new learning algorithms for the design of prediction systems by directly optimising the correlation coefficient. We observe and prove several results relating sensitivity and specificity of optimal systems. While the principles are general, we illustrate the applicability on specific problems such as protein secondary structure and signal peptide prediction.'),
(69757, 2000, 'bio', 'Prediction of genetic structure in eukaryotic DNA using reference point logistic regression and sequence alignment', 'Hooper, P M|Zhang, H|Wishart, D S', 'Department of Mathematical Sciences, University of Alberta, Edmonton, AB, Canada T6G 2G1. hooper@stat.ualberta.ca|Department of Mathematical Sciences, University of Alberta, Edmonton, AB, Canada T6G 2G1. hooper@stat.ualberta.ca|Department of Mathematical Sciences, University of Alberta, Edmonton, AB, Canada T6G 2G1. hooper@stat.ualberta.ca', 'Canada|Canada|Canada', 11, 'Algorithms|Animals|Arabidopsis|Base Composition|DNA|DNA, Plant|Databases, Factual|Drosophila|Humans|Logistic Models|Markov Chains|Models, Genetic|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/16.5.425', '10871265', 'Current software tools are moderately effective in predicting genetic structure (exons, introns, intergenic regions, and complete genes) from raw DNA sequence data. Improvements in accuracy and speed are needed to deal with the increasing volume of data from large scale sequencing projects.'),
(69758, 2000, 'bio', 'PatSearch: a pattern matcher software that finds functional elements in nucleotide and protein sequences and assesses their statistical significance', 'Pesole, G|Liuni, S|DSouza, M', 'Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, Via Celoria, 26, 20133 Milano, Italy. graziano.pesole@unimi.it|Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, Via Celoria, 26, 20133 Milano, Italy. graziano.pesole@unimi.it|Dipartimento di Fisiologia e Biochimica Generali, Università di Milano, Via Celoria, 26, 20133 Milano, Italy. graziano.pesole@unimi.it', 'Italy|Italy|Italy', 71, '3 Untranslated Regions|5 Untranslated Regions|Algorithms|Amino Acid Sequence|Animals|Base Sequence|Computer Simulation|DNA|Databases, Factual|Histones|Humans|Nucleic Acid Conformation|Pattern Recognition, Automated|RNA, Messenger|Sensitivity and Specificity|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/16.5.439', '10871266', 'The identification of sequence patterns involved in gene regulation and expression is a major challenge in molecular biology. In this paper we describe a novel algorithm and the software for searching nucleotide and protein sequences for complex nucleotide patterns including potential secondary structure elements, also allowing for mismatches/mispairings below a user-fixed threshold, and assessing the statistical significance of their occurrence through a Markov chain simulation.'),
(69759, 2000, 'bio', 'GeneRAGE: a robust algorithm for sequence clustering and domain detection', 'Enright, A J|Ouzounis, C A', 'Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.|Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.', 'United Kingdom|United Kingdom', 0, 'Algorithms|Amino Acid Sequence|Bacterial Proteins|Cluster Analysis|Databases, Factual|Fungal Proteins|Genome, Bacterial|Genome, Fungal|Protein Structure, Tertiary|Proteins|Sequence Alignment', 'Journal Article', '10.1093/bioinformatics/16.5.451', '10871267', 'Efficient, accurate and automatic clustering of large protein sequence datasets, such as complete proteomes, into families, according to sequence similarity. Detection and correction of false positive and negative relationships with subsequent detection and resolution of multi-domain proteins.'),
(69760, 2000, 'bio', 'RSDB: representative protein sequence databases have high information content', 'Park, J|Holm, L|Heger, A|Chothia, C', 'The European Bioinformatics Institute, EMBL Outstation, Cambridge CB10 1SD, UK. jong@biosophy.org|The European Bioinformatics Institute, EMBL Outstation, Cambridge CB10 1SD, UK. jong@biosophy.org|The European Bioinformatics Institute, EMBL Outstation, Cambridge CB10 1SD, UK. jong@biosophy.org|The European Bioinformatics Institute, EMBL Outstation, Cambridge CB10 1SD, UK. jong@biosophy.org', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom', 35, 'Algorithms|Amino Acid Sequence|Databases, Factual|Gene Duplication|Proteins|Sequence Alignment|Sequence Homology, Amino Acid', 'Comparative Study', '10.1093/bioinformatics/16.5.458', '10871268', 'Biological sequence databases are highly redundant for two main reasons: 1. various databanks keep redundant sequences with many identical and nearly identical sequences 2. natural sequences often have high sequence identities due to gene duplication. We wanted to know how many sequences can be removed before the databases start losing homology information. Can a database of sequences with mutual sequence identity of 50% or less provide us with the same amount of biological information as the original full database?'),
(69761, 2000, 'bio', 'BIND--a data specification for storing and describing biomolecular interactions, molecular complexes and pathways', 'Bader, G D|Hogue, C W', 'Department of Biochemistry, University of Toronto/Samuel Lunenfeld Research Institute, Toronto, M5G 1X5, Canada Samuel Lunenfeld Research Institute, Toronto, M5G 1X5, Canada.|Department of Biochemistry, University of Toronto/Samuel Lunenfeld Research Institute, Toronto, M5G 1X5, Canada Samuel Lunenfeld Research Institute, Toronto, M5G 1X5, Canada.', 'Canada|Canada', 142, 'DNA|Databases, Factual|Humans|Macromolecular Substances|Models, Statistical|Molecular Biology|Proteins|RNA', 'Journal Article', '10.1093/bioinformatics/16.5.465', '10871269', 'Proteomics is gearing up towards high-throughput methods for identifying and characterizing all of the proteins, protein domains and protein interactions in a cell and will eventually create more recorded biological information than the Human Genome Project. Each protein expressed in a cell can interact with various other proteins and molecules in the course of its function. A standard data specification is required that can describe and store this information in all its detail and allow efficient cross-platform transfer of data. A complete specification must be the basis for any database or tool for managing and analysing this information.'),
(69762, 2000, 'bio', 'A homolog of mammalian antizyme is present in fission yeast Schizosaccharomyces pombe but not detected in budding yeast Saccharomyces cerevisiae', 'Zhu, C|Karplus, K|Grate, L|Coffino, P', 'Department of Microbiology and Immunology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.|Department of Microbiology and Immunology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.|Department of Microbiology and Immunology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.|Department of Microbiology and Immunology, University of California, Santa Cruz, Santa Cruz, CA 95064, USA.', 'United States|United States|United States|United States', 9, 'Amino Acid Sequence|Animals|Conserved Sequence|Enzyme Inhibitors|Fungal Proteins|Genome, Fungal|Humans|Molecular Sequence Data|Ornithine Decarboxylase Inhibitors|Proteins|Saccharomyces cerevisiae|Schizosaccharomyces|Sequence Homology, Amino Acid|Species Specificity', 'Comparative Study', '10.1093/bioinformatics/16.5.478', '10871270', 'The antizymes (AZ) are proteins that regulate cellular polyamine pools in metazoa. To search for remote homologs in single-celled eukaryotes, we used computer software based on hidden Markov models. The most divergent homolog detected was that of the fission yeast Schizosaccharomyces pombe. Sequence identities between S.POMBE: AZ and known AZs are as low as 18-22% in the most conserved C-terminal regions. The authenticity of the S.POMBE: AZ is validated by the presence of a conserved nucleotide sequence that, in metazoa, promotes a +1 programmed ribosomal frameshift required for AZ expression. However, no homolog was detected in the completed genome of the budding yeast Saccharomyces cerevisiae. Procedural details and supplementary information can be found at http://itsa.ucsf.edu/ approximately czhu/AZ.'),
(69763, 2000, 'bio', 'GESTALT: a workbench for automatic integration and visualization of large-scale genomic sequence analyses', 'Glusman, G|Lancet, D', 'Department of Molecular Genetics and the Crown Human Genome Center, The Weizmann Institute of Science, Rehovot 76100, Israel. Gustavo@bioinfo.weizmann.ac.il|Department of Molecular Genetics and the Crown Human Genome Center, The Weizmann Institute of Science, Rehovot 76100, Israel. Gustavo@bioinfo.weizmann.ac.il', 'Israel|Israel', 30, 'Algorithms|Chromosome Mapping|Computer Graphics|Genome|Internet|Sequence Analysis|Software', 'Journal Article', '10.1093/bioinformatics/16.5.482', '10871271', 'The GESTALT Workbench is a WWW-based tool for genomic sequence analysis, comparison and annotation, with strong emphasis on visualization. GESTALT integrates graphically the output of diverse sequence analysis algorithms producing an information-rich, interactive genomic map.'),
(69764, 2000, 'bio', 'Viral Genome DataBase: storing and analyzing genes and proteins from complete viral genomes', 'Hiscock, D|Upton, C', 'Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055, Victoria, BC V8W 3P6, Canada.|Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055, Victoria, BC V8W 3P6, Canada.', 'Canada|Canada', 26, 'Databases, Factual|Genes, Viral|Genome, Viral|Internet|Viral Proteins', 'Journal Article', '10.1093/bioinformatics/16.5.484', '10871272', 'The Viral Genome DataBase (VGDB) contains detailed information of the genes and predicted protein sequences from 15 completely sequenced genomes of large (&100 kb) viruses (2847 genes). The data that is stored includes DNA sequence, protein sequence, GenBank and user-entered notes, molecular weight (MW), isoelectric point (pI), amino acid content, A + T%, nucleotide frequency, dinucleotide frequency and codon use. The VGDB is a mySQL database with a user-friendly JAVA GUI. Results of queries can be easily sorted by any of the individual parameters.'),
(69765, 2000, 'bio', 'RadCon: phylogenetic tree comparison and consensus', 'Thorley, J L|Page, R D', 'School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK. j.l.thorey@bris.ac.uk|School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK. j.l.thorey@bris.ac.uk', 'United Kingdom|United Kingdom', 111, 'Phylogeny|Software', 'Comparative Study', '10.1093/bioinformatics/16.5.486', '10871273', 'RadCon is a Macintosh program for manipulating and analysing phylogenetic trees. The program can determine the Cladistic Information Content of individual trees, the stability of leaves across a set of bootstrap trees, produce the strict basic Reduced Cladistic Consensus profile of a set of trees and convert a set of trees into its matrix representation for supertree construction.'),
(69766, 2000, 'bio', 'Concerning the accuracy of MAST E-values', 'Bailey, T L|Gribskov, M', 'School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK. j.l.thorey@bris.ac.uk|School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK. j.l.thorey@bris.ac.uk', 'United Kingdom|United Kingdom', 9, 'Algorithms|Databases, Factual|Reproducibility of Results|Sequence Alignment|Software', 'Comment', '10.1093/bioinformatics/16.5.488', '10871274', '-'),
(69767, 2000, 'bio', 'Analyse thisor: intelligent help for the rest of us', 'Fuchs, R', 'School of Biological Sciences, University of Bristol, Bristol BS8 1UG, UK. j.l.thorey@bris.ac.uk', 'United Kingdom', 1, 'Computational Biology|Data Interpretation, Statistical|Sequence Analysis|Software', 'Editorial', '10.1093/bioinformatics/16.6.491', '10980145', '-'),
(69768, 2000, 'bio', 'A case study in genome-level fragment assembly', 'Chen, T|Skiena, S S', 'Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. tchen@arep.med.harvard.edu|Department of Genetics, Harvard Medical School, Boston, MA 02115, USA. tchen@arep.med.harvard.edu', 'United States|United States', 24, 'Algorithms|Borrelia burgdorferi Group|Computational Biology|DNA, Bacterial|Databases, Factual|Genome, Bacterial|Sequence Alignment|Sequence Analysis, DNA|Software', 'Comparative Study', '10.1093/bioinformatics/16.6.494', '10980146', 'We use the fact of two teams independently sequencing the one megabase genome of Borrelia burgdorferi as an opportunity to study the accuracy of genome-level assembly.'),
(69769, 2000, 'bio', 'Phylogenetically enhanced statistical tools for RNA structure prediction', 'Akmaev, V R|Kelley, S T|Stormo, G D', 'Dept. of Applied Mathematics, Box 526, University of Colorado, Boulder, CO 80309, USA.|Dept. of Applied Mathematics, Box 526, University of Colorado, Boulder, CO 80309, USA.|Dept. of Applied Mathematics, Box 526, University of Colorado, Boulder, CO 80309, USA.', 'United States|United States|United States', 39, 'Base Sequence|Biometry|Escherichia coli|Evolution, Molecular|Likelihood Functions|Models, Genetic|Molecular Sequence Data|Nucleic Acid Conformation|Phylogeny|RNA|RNA, Bacterial|RNA, Ribosomal, 16S|Sequence Analysis, RNA', 'Comparative Study', '10.1093/bioinformatics/16.6.501', '10980147', 'Methods that predict the structure of molecules by looking for statistical correlation have been quite effective. Unfortunately, these methods often disregard phylogenetic information in the sequences they analyze. Here, we present a number of statistics for RNA molecular-structure prediction. Besides common pair-wise comparisons, we consider a few reasonable statistics for base-triple predictions, and present an elaborate analysis of these methods. All these statistics incorporate phylogenetic relationships of the sequences in the analysis to varying degrees, and the different nature of these tests gives a wide choice of statistical tools for RNA structure prediction.'),
(69770, 2000, 'bio', 'Browsing the SLoop database of structurally classified loops connecting elements of protein secondary structure', 'Burke, D F|Deane, C M|Blundell, T L', 'Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB1 2GA1, UK.|Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB1 2GA1, UK.|Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB1 2GA1, UK.', 'United Kingdom|United Kingdom|United Kingdom', 37, 'Amino Acid Sequence|Databases, Factual|Internet|Models, Molecular|Molecular Sequence Data|Peptide Fragments|Protein Conformation|Protein Structure, Secondary|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/16.6.513', '10980148', 'We describe a web server, which provides easy access to the SLoop database of loop conformations connecting elements of protein secondary structure. The loops are classified according to their length, the type of bounding secondary structures and the conformation of the mainchain. The current release of the database consists of over 8000 loops of up to 20 residues in length. A loop prediction method, which selects conformers on the basis of the sequence and the positions of the elements of secondary structure, is also implemented. These web pages are freely accessible over the internet at http://www-cryst.bioc.cam.ac.uk/ approximately sloop.'),
(69771, 2000, 'bio', 'Quick selection of representative protein chain sets based on customizable requirements', 'Noguchi, T|Onizuka, K|Ando, M|Matsuda, H|Akiyama, Y', 'Parallel Application TRC Laboratory, Real World Computing Partnership, Tsukuba Mitsui Building 1-6-1 Takezono, Tsukuba-shi Ibaraki 305-0032, Japan.|Parallel Application TRC Laboratory, Real World Computing Partnership, Tsukuba Mitsui Building 1-6-1 Takezono, Tsukuba-shi Ibaraki 305-0032, Japan.|Parallel Application TRC Laboratory, Real World Computing Partnership, Tsukuba Mitsui Building 1-6-1 Takezono, Tsukuba-shi Ibaraki 305-0032, Japan.|Parallel Application TRC Laboratory, Real World Computing Partnership, Tsukuba Mitsui Building 1-6-1 Takezono, Tsukuba-shi Ibaraki 305-0032, Japan.|Parallel Application TRC Laboratory, Real World Computing Partnership, Tsukuba Mitsui Building 1-6-1 Takezono, Tsukuba-shi Ibaraki 305-0032, Japan.', 'Japan|Japan|Japan|Japan|Japan', 4, 'Databases, Factual|Internet|Models, Molecular|Protein Conformation|Proteins|Software Design', 'Journal Article', '10.1093/bioinformatics/16.6.520', '10980149', 'Protein structure classification has been recognized as one of the most important research issues in protein structure analysis. A substantial number of methods for the classification have been proposed, and several databases have been constructed using these methods. Since some proteins with very similar sequences may exhibit structural diversities, we have proposed PDB-REPRDB: a database of representative protein chains from the Protein Data Bank (PDB), which strategy of selection is based not only on sequence similarity but also on structural similarity. Forty-eight representative sets whose similarity criteria were predetermined were made available over the World Wide Web (WWW). However, the sets were insufficient in number to satisfy users researching protein structures by various methods.'),
(69772, 2000, 'bio', 'Comparing systemic properties of ensembles of biological networks by graphical and statistical methods', 'Alves, R|Savageau, M A', 'Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II Ann Arbor, MI 48109-0620, USA.|Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II Ann Arbor, MI 48109-0620, USA.', 'United States|United States', 36, 'Biometry|Computational Biology|Models, Biological', 'Comparative Study', '10.1093/bioinformatics/16.6.527', '10980150', 'When dealing with questions that concern a general class of models for biological networks, large numbers of distinct models within the class can be grouped into an ensemble that gives a statistical view of the properties for the general class. Comparing properties of different ensembles through the use of point measures (e.g. medians, standard deviations, correlation coefficients) can mask inhomogeneities in the correlations between properties. We are therefore motivated to develop strategies that allow these inhomogeneities to be more easily detected.'),
(69773, 2000, 'bio', 'Systemic properties of ensembles of metabolic networks: application of graphical and statistical methods to simple unbranched pathways', 'Alves, R|Savageau, M A', 'Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II Ann Arbor, MI 48109-0620 USA.|Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II Ann Arbor, MI 48109-0620 USA.', 'United States|United States', 47, 'Amino Acids|Biometry|Computational Biology|Feedback|Metabolism|Models, Biological', 'Comparative Study', '10.1093/bioinformatics/16.6.534', '10980151', 'Mathematical models are the only realistic method for representing the integrated dynamic behavior of complex biochemical networks. However, it is difficult to obtain a consistent set of values for the parameters that characterize such a model. Even when a set of parameter values exists, the accuracy of the individual values is questionable. Therefore, we were motivated to explore statistical techniques for analyzing the properties of a given model when knowledge of the actual parameter values is lacking.'),
(69774, 2000, 'bio', 'Conceptual modelling of genomic information', 'Paton, N W|Khan, S A|Hayes, A|Moussouni, F|Brass, A|Eilbeck, K|Goble, C A|Hubbard, S J|Oliver, S G', 'Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK. norm@cs.man.ac.uk|Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK. norm@cs.man.ac.uk|Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK. norm@cs.man.ac.uk|Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK. norm@cs.man.ac.uk|Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK. norm@cs.man.ac.uk|Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK. norm@cs.man.ac.uk|Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK. norm@cs.man.ac.uk|Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK. norm@cs.man.ac.uk|Department of Computer Science, University of Manchester, Oxford Road, Manchester M13 9PL, UK. norm@cs.man.ac.uk', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom', 81, 'Computational Biology|Database Management Systems|Databases, Factual|Genome|Models, Genetic|Proteins|Sequence Analysis, DNA|Transcription, Genetic', 'Journal Article', '10.1093/bioinformatics/16.6.548', '10980152', 'Genome sequencing projects are making available complete records of the genetic make-up of organisms. These core data sets are themselves complex, and present challenges to those who seek to store, analyse and present the information. However, in addition to the sequence data, high throughput experiments are making available distinctive new data sets on protein interactions, the phenotypic consequences of gene deletions, and on the transcriptome, proteome, and metabolome. The effective description and management of such data is of considerable importance to bioinformatics in the post-genomic era. The provision of clear and intuitive models of complex information is surprisingly challenging, and this paper presents conceptual models for a range of important emerging information resources in bioinformatics. It is hoped that these can be of benefit to bioinformaticians as they attempt to integrate genetic and phenotypic data with that from genomic sequences, in order to both assign gene functions and elucidate the different pathways of gene action and interaction.'),
(69775, 2000, 'bio', 'IMpRH server: an RH mapping server available on the Web', 'Milan, D|Hawken, R|Cabau, C|Leroux, S|Genet, C|Lahbib, Y|Tosser, G|Robic, A|Hatey, F|Alexander, L|Beattie, C|Schook, L|Yerle, M|Gellin, J', 'Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr|Laboratoire de Génétique Cellulaire, INRA, BP27, 31326 Castanet-Tolosan, France. milan@toulouse.inra.fr', 'France|France|France|France|France|France|France|France|France|France|France|France|France|France', 237, 'Animals|Chromosome Mapping|Computational Biology|Databases, Factual|Genetic Markers|Hybrid Cells|Internet|Swine', 'Journal Article', '10.1093/bioinformatics/16.6.558', '10980153', 'The INRA-Minnesota Porcine Radiation Hybrid (IMpRH) Server provides both a mapping tool (IMpRH mapping tool) and a database (IMpRH database) of officially submitted results. The mapping tool permits the mapping of a new marker relatively to markers previously mapped on the IMpRH panel. The IMpRH database is the official database for submission of new results and queries. The database not only permits the sharing of public data but also semi-private and private data.'),
(69776, 2000, 'bio', 'Oriloc: prediction of replication boundaries in unannotated bacterial chromosomes', 'Frank, A C|Lobry, J R', 'Laboratoire BBE-CNRS UMR 5558, UniversitéClaude Bernard, 43 Bd. du 11 Novembre 1918, F-69622 Villeurbanne cedex, France.|Laboratoire BBE-CNRS UMR 5558, UniversitéClaude Bernard, 43 Bd. du 11 Novembre 1918, F-69622 Villeurbanne cedex, France.', 'France|France', 0, 'Chlamydia trachomatis|Chromosomes, Bacterial|Computational Biology|DNA Replication|Genome, Bacterial|Software', 'Journal Article', '10.1093/bioinformatics/16.6.560', '10980154', 'A program called Oriloc has been developed for the prediction of bacterial replication origins. The method builds on the fact that there are compositional asymmetries between the leading and the lagging strand for replication. The program works with unannotated sequences in fasta format and therefore uses glimmer 2.0 outputs to discriminate between codon positions so as to increase the signal/noise ratio.'),
(69777, 2000, 'bio', 'RDP: detection of recombination amongst aligned sequences', 'Martin, D|Rybicki, E', 'Microbiology Department, University of Cape Town, Private Bag, Cape Town, South Africa.|Microbiology Department, University of Cape Town, Private Bag, Cape Town, South Africa.', 'South Africa|South Africa', 1021, 'Computational Biology|DNA, Viral|Genome, Viral|HIV|Recombination, Genetic|Sequence Alignment|Simian Immunodeficiency Virus|Software', 'Comparative Study', '10.1093/bioinformatics/16.6.562', '10980155', 'Recombination Detection Program (RDP) is a program that applies a pairwise scanning approach to the detection of recombination amongst a group of aligned DNA sequences. The software runs under Windows95 and combines highly automated screening of large numbers of sequences with a highly interactive interface for examining the results of the analyses.'),
(69778, 2000, 'bio', 'Disperse: a simple and efficient approach to parallel database searching', 'Clifford, R|Mackey, A J', 'Department of Computing, Imperial College of Science, Technology and Medicine, London, UK. r.clifford@ic.ac.uk|Department of Computing, Imperial College of Science, Technology and Medicine, London, UK. r.clifford@ic.ac.uk', 'United Kingdom|United Kingdom', 15, 'Computational Biology|Databases, Factual|Sequence Alignment|Software', 'Comparative Study', '10.1093/bioinformatics/16.6.564', '10980156', 'A general system for performing multiple independent database searches in parallel is presented. Run-time addition and removal of clients, robust failure and error trapping and near 100% efficiency with very large numbers of clients are achieved by a flexible asynchronous, client-driven approach.'),
(69779, 2000, 'bio', 'DaliLite workbench for protein structure comparison', 'Holm, L|Park, J', 'holm@embl-ebi.ac.uk|holm@embl-ebi.ac.uk', '-|-', 759, 'Computational Biology|Databases, Factual|Internet|Models, Molecular|Proteins|Sequence Alignment|Software', 'Comparative Study', '10.1093/bioinformatics/16.6.566', '10980157', 'DaliLite is a program for pairwise structure comparison and for structure database searching. It is a standalone version of the search engine of the popular Dali server. A web interface is provided to view the results, multiple alignments and 3D superimpositions of structures.'),
(69780, 2000, 'bio', 'MIPSIM: similarity analysis of molecular interaction potentials', '-', '-', '-', 0, 'Computational Biology|Internet|Models, Molecular|Quantitative Structure-Activity Relationship|Software', 'Comparative Study', '10.1093/bioinformatics/16.6.568', '10980158', 'MIPSIM is a computational package designed to analyse and compare 3D distributions of molecular interaction potentials (MIP) of series of biomolecules.'),
(69781, 2000, 'bio', 'The economic value of bioinformation', 'Milosavljevic, A', 'holm@embl-ebi.ac.uk', '-', 0, 'Computational Biology|Drug Design|Humans|Models, Econometric|Patents as Topic', 'Editorial', '10.1093/bioinformatics/16.7.571', '11038327', '-'),
(69782, 2000, 'bio', 'Sister-scanning: a Monte Carlo procedure for assessing signals in recombinant sequences', 'Gibbs, M J|Armstrong, J S|Gibbs, A J', 'Research School of Biological Sciences, The Australian National University, GPO Box 475, Canberra ACT 2601, Australia. mgibbs@rsbs.anu.edu.au|Research School of Biological Sciences, The Australian National University, GPO Box 475, Canberra ACT 2601, Australia. mgibbs@rsbs.anu.edu.au|Research School of Biological Sciences, The Australian National University, GPO Box 475, Canberra ACT 2601, Australia. mgibbs@rsbs.anu.edu.au', 'Australia|Australia|Australia', 666, 'Computer Simulation|Luteovirus|Monte Carlo Method|RNA Replicase|Recombination, Genetic|Tobamovirus', 'Journal Article', '10.1093/bioinformatics/16.7.573', '11038328', 'To devise a method that, unlike available methods, directly measures variations in phylogenetic signals in gene sequences that result from recombination, tests the significance of the signal variations and distinguishes misleading signals.'),
(69783, 2000, 'bio', 'Secondary structure alone is generally not statistically significant for the detection of noncoding RNAs', 'Rivas, E|Eddy, S R', 'Department of Genetics, Washington University, St. Louis, MO 63110, USA.|Department of Genetics, Washington University, St. Louis, MO 63110, USA.', 'United States|United States', 0, 'Algorithms|Animals|Base Composition|Caenorhabditis elegans|Data Interpretation, Statistical|Methanococcus|Models, Statistical|Nucleic Acid Conformation|RNA|RNA, Helminth', 'Journal Article', '10.1093/bioinformatics/16.7.583', '11038329', 'Several results in the literature suggest that biologically interesting RNAs have secondary structures that are more stable than expected by chance. Based on these observations, we developed a scanning algorithm for detecting noncoding RNA genes in genome sequences, using a fully probabilistic version of the Zuker minimum-energy folding algorithm.'),
(69784, 2000, 'bio', 'Clustalnet: the joining of Clustal and CORBA', 'Campagne, F', 'Department of Physiology and Biophysics, Box 1218, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, NY 10029-6574, USA.', 'United States', 2, 'Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/16.7.606', '11038330', 'Performing sequence alignment operations from a different program than the original sequence alignment code, and/or through a network connection, is often required. Interactive alignment editors and large-scale biological data analysis are common examples where such a flexibility is important. Interoperability between the alignment engine and the client should be obtained regardless of the architectures and programming languages of the server and client.'),
(69785, 2000, 'bio', 'Domain size distributions can predict domain boundaries', 'Wheelan, S J|Marchler-Bauer, A|Bryant, S H', 'National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.|National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.|National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894, USA.', 'United States|United States|United States', 59, 'Algorithms|Models, Molecular|Probability|Protein Structure, Tertiary|Proteins', 'Journal Article', '10.1093/bioinformatics/16.7.613', '11038331', 'The sizes of protein domains observed in the 3D-structure database follow a surprisingly narrow distribution. Structural domains are furthermore formed from a single-chain continuous segment in over 80% of instances. These observations imply that some choices of domain boundaries on an otherwise uncharacterized sequence are more likely than others, based solely on the size and segment number of predicted domains. This property might be used to guess the locations of protein domain boundaries.'),
(69786, 2000, 'bio', 'Using traveling salesman problem algorithms for evolutionary tree construction', 'Korostensky, C|Gonnet, G H', 'Institute for Scientific Computing, 8092 ETH Zurich, Switzerland. chantal.roth@nobilitas.com|Institute for Scientific Computing, 8092 ETH Zurich, Switzerland. chantal.roth@nobilitas.com', 'Switzerland|Switzerland', 6, 'Algorithms|Amino Acid Sequence|Animals|Cytochrome P-450 CYP1A1|Cytochrome P-450 CYP1A2|Evolution, Molecular|Glycated Hemoglobin A|Molecular Sequence Data|Phylogeny|Sequence Analysis', 'Journal Article', '10.1093/bioinformatics/16.7.619', '11038332', 'The construction of evolutionary trees is one of the major problems in computational biology, mainly due to its complexity.'),
(69787, 2000, 'bio', 'Object-oriented parsing of biological databases with Python', 'Ramu, C|Gemünd, C|Gibson, T J', 'European Molecular Biological Laboratory, Meyerhofstrasse 1, Postfach 10.2209, Heidelberg, Germany. chenna@embl-heidelberg.de|European Molecular Biological Laboratory, Meyerhofstrasse 1, Postfach 10.2209, Heidelberg, Germany. chenna@embl-heidelberg.de|European Molecular Biological Laboratory, Meyerhofstrasse 1, Postfach 10.2209, Heidelberg, Germany. chenna@embl-heidelberg.de', 'Germany|Germany|Germany', 6, 'Databases, Factual|Programming Languages|Sequence Analysis', 'Journal Article', '10.1093/bioinformatics/16.7.628', '11038333', 'While database activities in the biological area are increasing rapidly, rather little is done in the area of parsing them in a simple and object-oriented way.'),
(69788, 2000, 'bio', 'Digital reviews in molecular biology: approaches to structured digital publication', 'Steffen, D L|Levine, A E|Yarus, S|Baasiri, R A|Wheeler, D A', 'Biomedical Computing, Inc., Houston, TX 77005, USA. steffen@biomedcomp.com|Biomedical Computing, Inc., Houston, TX 77005, USA. steffen@biomedcomp.com|Biomedical Computing, Inc., Houston, TX 77005, USA. steffen@biomedcomp.com|Biomedical Computing, Inc., Houston, TX 77005, USA. steffen@biomedcomp.com|Biomedical Computing, Inc., Houston, TX 77005, USA. steffen@biomedcomp.com', 'United States|United States|United States|United States|United States', 0, 'Algorithms|Animals|Databases, Factual|Humans|Internet|Molecular Biology|Mutation|Neoplasms|Periodicals as Topic|Publishing|Transgenes', 'Journal Article', '10.1093/bioinformatics/16.7.639', '11038334', 'It is widely appreciated that it is no longer possible for biomedical research scientists to keep up with as much of what is published in their field as they ought. One solution to this problem is to increase the efficiency of information use by moving away from the classical browsing model for scientific information dissemination towards an information on demand model which would allow researchers to access information quickly and efficiently only as they need it. The most common approach to this goal has been to use information retrieval technology to improve access to text databases of biomedical information. We are interested in exploring an alternative, encoding this information for storage in structured databases for efficient retrieval.'),
(69789, 2000, 'bio', 'eSAGE: managing and analysing data generated with serial analysis of gene expression (SAGE)', 'Margulies, E H|Innis, J W', 'Departments of Human Genetics Pediatrics & Communicable Diseases, University of Michigan Medical School Ann Arbor, Michigan 48109-0618, USA. ehm@umich.edu|Departments of Human Genetics Pediatrics & Communicable Diseases, University of Michigan Medical School Ann Arbor, Michigan 48109-0618, USA. ehm@umich.edu', 'United States|United States', 0, 'Databases, Factual|Gene Expression|Software', 'Journal Article', '10.1093/bioinformatics/16.7.650', '11038335', 'eSAGE is a comprehensive set of software tools for managing and analysing data generated with Serial Analysis of Gene Expression (SAGE).'),
(69790, 2000, 'bio', 'DNAssist: the integrated editing and analysis of molecular biology sequences in windows', 'Patterton, H G|Graves, S', 'Department of Biochemistry, University of Cape Town, University Private Bag, Rondebosch 7700, South Africa.|Department of Biochemistry, University of Cape Town, University Private Bag, Rondebosch 7700, South Africa.', 'South Africa|South Africa', 0, 'Animals|Humans|Restriction Mapping|Sequence Alignment|Sequence Analysis|Sequence Analysis, DNA|Sequence Analysis, Protein|Sequence Analysis, RNA|Software', 'Journal Article', '10.1093/bioinformatics/16.7.652', '11038336', 'The programs currently available for the analysis of nucleic acid and protein sequences suffer from a variety of problems: Web-based programs often require inconvenient reformatting of sequences when proceeding from one analysis to the next, and commercial-console-based programs are cost prohibitive. Here, we report the development of DNASSIST:, an inexpensive, multiple-document, interface program for the fully integrated editing and analysis of nucleic acid and protein sequences in the familiar environment of Microsoft Windows.'),
(69791, 2000, 'bio', 'A cross-comparison of a large dataset of genes', 'Cannarozzi, G|Hallett, M T|Norberg, J|Zhou, X', 'Department of Chemistry, University of Florida, Gainesville 32611,|Department of Chemistry, University of Florida, Gainesville 32611,|Department of Chemistry, University of Florida, Gainesville 32611,|Department of Chemistry, University of Florida, Gainesville 32611,', '-|-|-|-', 5, 'Animals|Humans|Proteins|Sequence Alignment', 'Journal Article', '10.1093/bioinformatics/16.7.654', '11038337', 'We make available a large cross-comparison for 16 of the completely sequenced genomes and additional eukaryotic genes. The alignments were performed at the protein level using liberal similarity bounds in order to capture as many significant alignments as possible. This dataset will be updated as new genomes become available.'),
(69792, 2000, 'bio', 'NAIL-Network Analysis Interface for Linking HMMER results', 'Sánchez-Pulido, L|Yuan, Y P|Andrade, M A|Bork, P', 'Protein Design Group, Centro Nacional de Biotecnología (CNB-CSIC), Campus Univ. Autónoma, Cantoblanco 28049, Madrid, Spain. sanchez@cnb.uam.es|Protein Design Group, Centro Nacional de Biotecnología (CNB-CSIC), Campus Univ. Autónoma, Cantoblanco 28049, Madrid, Spain. sanchez@cnb.uam.es|Protein Design Group, Centro Nacional de Biotecnología (CNB-CSIC), Campus Univ. Autónoma, Cantoblanco 28049, Madrid, Spain. sanchez@cnb.uam.es|Protein Design Group, Centro Nacional de Biotecnología (CNB-CSIC), Campus Univ. Autónoma, Cantoblanco 28049, Madrid, Spain. sanchez@cnb.uam.es', 'Spain|Spain|Spain|Spain', 0, 'Databases, Factual|Internet|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/16.7.656', '11038338', 'Network Analysis Interface for Linking HMMER results (NAIL) is a web-based tool for the analysis of results from a HMMER protein database-search. NAIL facilitates the selection of protein hits and the creation of an alignment, which can be used for a new sequence similarity search.'),
(69793, 2000, 'bio', 'SChiSM: creating interactive web page annotations of molecular structure models using chime', 'Cammer, S A', 'The Laboratory for Molecular Modeling, Division of Medicinal Chemistry and Natural Products, School of Pharmacy, University of North Carolina at Chapel Hill, USA. cammer@email.unc.edu', 'United States', 5, 'Computer Graphics|Internet|Models, Molecular|Software', 'Journal Article', '10.1093/bioinformatics/16.7.658', '11038339', 'SChiSM is a program for creating World Wide Web (WWW) pages that include embedded interactive molecular models using the browser plug-in, CHIME:, for visualization. The program works with Netscape 4.x and Internet Explorer 5 browsers to facilitate Chime/Rasmol scripting control of a molecular display.'),
(69794, 2000, 'bio', 'Visualizing large hierarchical clusters in hyperbolic space', 'Bingham, J|Sudarsanam, S', 'SUGEN, 230 East Grand Avenue, South San Francisco, CA 94080, USA.|SUGEN, 230 East Grand Avenue, South San Francisco, CA 94080, USA.', 'United States|United States', 0, 'Animals|Caenorhabditis elegans|Gene Expression|Phylogeny|Protein Kinases|Proteins|Software|Vision, Ocular', 'Journal Article', '10.1093/bioinformatics/16.7.660', '11038340', 'HyperTree is an application to visualize and navigate large trees in hyperbolic space. It includes color-coding, search mechanisms and navigational aids, as well as focus+context viewing, allowing enormous trees to fit within the fixed space of a computer screen or printed page.'),
(69795, 2000, 'bio', 'Bioinformatics--the necessity of the quest for first principles in life', 'Wada, A', 'SUGEN, 230 East Grand Avenue, South San Francisco, CA 94080, USA.', 'United States', 5, 'Computational Biology|DNA|Humans', 'Editorial', '10.1093/bioinformatics/16.8.663', '11099252', '-'),
(69796, 2000, 'bio', 'A systematic approach to dynamic programming in bioinformatics', 'Giegerich, R', 'Faculty of Technology, Bielefeld University, 33615 Bielefeld, Germany. robert@techfak.uni-bielefeld.de', 'Germany', 0, 'Algorithms|Computational Biology|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/16.8.665', '11099253', 'Dynamic programming is probably the most popular programming method in bioinformatics. Sequence comparison, gene recognition, RNA structure prediction and hundreds of other problems are solved by ever new variants of dynamic programming. Currently, the development of a successful dynamic programming algorithm is a matter of experience, talent and luck. The typical matrix recurrence relations that make up a dynamic programming algorithm are intricate to construct, and difficult to implement reliably. No general problem independent guidance is available.'),
(69797, 2000, 'bio', 'ComboScreen facilitates the multiplex hybridization-based screening of high-density clone arrays', 'Jamison, D C|Thomas, J W|Green, E D', 'Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. cjamison@informaxinc.com|Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. cjamison@informaxinc.com|Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA. cjamison@informaxinc.com', 'United States|United States|United States', 12, 'Chromosomes, Artificial, Bacterial|Contig Mapping|Oligonucleotide Array Sequence Analysis|Software', 'Journal Article', '10.1093/bioinformatics/16.8.678', '11099254', 'The construction of physical maps based on bacterial clones [e.g. bacterial artificial chromosomes (BACs)] is valuable for a number of molecular genetics applications, including the high-resolution mapping of genomic regions of interest and the identification of clones suitable for systematic sequencing. A common approach for large-scale screening of bacterial clone libraries involves the hybridization of high-density arrays of immobilized, lysed colonies with collections of DNA probes. The use of a multiplex hybridization screening strategy, whereby pooled probes are analysed en masse, simplifies the effort by reducing the total number of parallel experiments required. However, this approach generates large amounts of hybridization-based data that must be carefully analysed, assimilated, and disambiguated in a careful but efficient manner.'),
(69798, 2000, 'bio', 'Generation of patterns from gene expression data by assigning confidence to differentially expressed genes', 'Manduchi, E|Grant, G R|McKenzie, S E|Overton, G C|Surrey, S|Stoeckert, C J', 'Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA. manduchi@pcbi.upenn.edu|Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA. manduchi@pcbi.upenn.edu|Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA. manduchi@pcbi.upenn.edu|Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA. manduchi@pcbi.upenn.edu|Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA. manduchi@pcbi.upenn.edu|Center for Bioinformatics, University of Pennsylvania, Philadelphia, PA 19104, USA. manduchi@pcbi.upenn.edu', 'United States|United States|United States|United States|United States|United States', 0, 'Algorithms|Databases, Factual|Gene Expression Profiling|Humans|Leukemia, Erythroblastic, Acute|Nylons|Oligonucleotide Array Sequence Analysis|Tumor Cells, Cultured', 'Journal Article', '10.1093/bioinformatics/16.8.685', '11099255', 'A protocol is described to attach expression patterns to genes represented in a collection of hybridization array experiments. Discrete values are used to provide an easily interpretable description of differential expression. Binning cutoffs for each sample type are chosen automatically, depending on the desired false-positive rate for the predictions of differential expression. Confidence levels are derived for the statement that changes in observed levels represent true changes in expression. We have a novel method for calculating this confidence, which gives better results than the standard methods. Our method reflects the broader change of focus in the field from studying a few genes with many replicates to studying many (possibly thousands) of genes simultaneously, but with relatively few replicates. Our approach differs from standard methods in that it exploits the fact that there are many genes on the arrays. These are used to estimate for each sample type an appropriate distribution that is employed to control the false-positive rate of the predictions made. Satisfactory results can be obtained using this method with as few as two replicates.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(69799, 2000, 'bio', 'Six-fold speed-up of Smith-Waterman sequence database searches using parallel processing on common microprocessors', 'Rognes, T|Seeberg, E', 'Institute of Medical Microbiology, University of Oslo, The National Hospital, NO-0027 Oslo, Norway. torbjorn.rognes@labmed.uio.no|Institute of Medical Microbiology, University of Oslo, The National Hospital, NO-0027 Oslo, Norway. torbjorn.rognes@labmed.uio.no', 'Norway|Norway', 0, 'Algorithms|Computing Methodologies|Databases, Factual|Microcomputers|Sequence Alignment|Time Factors', 'Journal Article', '10.1093/bioinformatics/16.8.699', '11099256', 'Sequence database searching is among the most important and challenging tasks in bioinformatics. The ultimate choice of sequence-search algorithm is that of Smith-Waterman. However, because of the computationally demanding nature of this method, heuristic programs or special-purpose hardware alternatives have been developed. Increased speed has been obtained at the cost of reduced sensitivity or very expensive hardware.'),
(69800, 2000, 'bio', 'Genetic network inference: from co-expression clustering to reverse engineering', 'Dhaeseleer, P|Liang, S|Somogyi, R', 'University of New Mexico, Department of Computer Science, Albuquerque, NM 87131, USA. patrik@cs.umm.edu|University of New Mexico, Department of Computer Science, Albuquerque, NM 87131, USA. patrik@cs.umm.edu|University of New Mexico, Department of Computer Science, Albuquerque, NM 87131, USA. patrik@cs.umm.edu', 'Mexico|Mexico|Mexico', 687, 'Animals|Cluster Analysis|Computer Simulation|Computing Methodologies|Databases, Factual|Gene Expression Regulation|Genomics|Information Storage and Retrieval|Linear Models|Neural Networks (Computer)|Nonlinear Dynamics', 'Journal Article', '10.1093/bioinformatics/16.8.707', '11099257', 'Advances in molecular biological, analytical and computational technologies are enabling us to systematically investigate the complex molecular processes underlying biological systems. In particular, using high-throughput gene expression assays, we are able to measure the output of the gene regulatory network. We aim here to review datamining and modeling approaches for conceptualizing and unraveling the functional relationships implicit in these datasets. Clustering of co-expression profiles allows us to infer shared regulatory inputs and functional pathways. We discuss various aspects of clustering, ranging from distance measures to clustering algorithms and multiple-cluster memberships. More advanced analysis aims to infer causal connections between genes directly, i.e. who is regulating whom and how. We discuss several approaches to the problem of reverse engineering of genetic networks, from discrete Boolean networks, to continuous linear and non-linear models. We conclude that the combination of predictive modeling with systematic experimental verification will be required to gain a deeper insight into living organisms, therapeutic targeting and bioengineering.'),
(69801, 2000, 'bio', 'Inferring qualitative relations in genetic networks and metabolic pathways', 'Akutsu, T|Miyano, S|Kuhara, S', 'Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. takutsu@ims.u-tokyo.ac.jp|Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. takutsu@ims.u-tokyo.ac.jp|Human Genome Center, Institute of Medical Science, University of Tokyo, 4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639, Japan. takutsu@ims.u-tokyo.ac.jp', 'Japan|Japan|Japan', 0, 'Algorithms|Computer Simulation|Computing Methodologies|Gene Expression Profiling|Genomics|Mathematical Computing|Metabolism', 'Journal Article', '10.1093/bioinformatics/16.8.727', '11099258', 'Inferring genetic network architecture from time series data of gene expression patterns is an important topic in bioinformatics. Although inference algorithms based on the Boolean network were proposed, the Boolean network was not sufficient as a model of a genetic network.'),
(69802, 2000, 'bio', 'In silico identification of transcripts and SNPs from a region of 4p linked with bipolar affective disorder', 'Semple, C A|Morris, S W|Porteous, D J|Evans, K L', 'M.R.C. Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK. c.semple@hgu.mrc.ac.uk|M.R.C. Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK. c.semple@hgu.mrc.ac.uk|M.R.C. Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK. c.semple@hgu.mrc.ac.uk|M.R.C. Human Genetics Unit, Western General Hospital, Edinburgh EH4 2XU, UK. c.semple@hgu.mrc.ac.uk', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom', 2, 'Bipolar Disorder|Chromosomes, Human, Pair 4|Databases, Factual|Expressed Sequence Tags|Genetic Linkage|Genetic Markers|Humans|Polymorphism, Single Nucleotide|RNA, Messenger', 'Journal Article', '10.1093/bioinformatics/16.8.735', '11099259', '-'),
(69803, 2000, 'bio', 'TRES: comparative promoter sequence analysis', 'Katti, M V|Sakharkar, M K|Ranjekar, P K|Gupta, V S', 'Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune 411 008, India.|Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune 411 008, India.|Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune 411 008, India.|Plant Molecular Biology Unit, Division of Biochemical Sciences, National Chemical Laboratory, Pune 411 008, India.', 'India|India|India|India', 0, 'Animals|Binding Sites|Humans|Promoter Regions, Genetic|Sequence Analysis, DNA|Software|Transcription Factors', 'Journal Article', '10.1093/bioinformatics/16.8.739', '11099260', 'Comparative promoter analysis is a promising strategy for elucidation of common regulatory modules conserved in evolutionarily related sequences or in genes showing common expression profiles. To facilitate such analysis, we have developed a software tool that detects conserved transcription factor binding sites, cis-elements, palindromes and k-tuples simultaneously in a set of sequences, and thus helps to identify putative motifs for designing further experiments.'),
(69804, 2000, 'bio', 'A comparison of signal sequence prediction methods using a test set of signal peptides', 'Menne, K M|Hermjakob, H|Apweiler, R', 'EMBL Outstation Hinxton - The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.|EMBL Outstation Hinxton - The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.|EMBL Outstation Hinxton - The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB10 1SD, UK.', 'United Kingdom|United Kingdom|United Kingdom', 106, 'Protein Sorting Signals|Software', 'Comparative Study', '10.1093/bioinformatics/16.8.741', '11099261', 'We describe the creation of a test set containing secretory and non-secretory proteins. Five existing prediction programs for signal sequences and their cleavage sites are compared on the basis of this test set: SPScan, SigCleave, SignalP V1.1, SignalP V2.0. b2-HMM and SignalP V2.0.b2-NN.'),
(69805, 2000, 'bio', 'gff2ps: visualizing genomic annotations', 'Abril, J F|Guigó, R', 'Grup de Recerca en Informàtica Mèdica, Institut Municipal dInvestigació Mèdica (IMIM), Universitat Pompeu Fabra (UPF), C/ Dr. Aiguader, 80. 08003-Barcelona, Spain. jabril@imim.es|Grup de Recerca en Informàtica Mèdica, Institut Municipal dInvestigació Mèdica (IMIM), Universitat Pompeu Fabra (UPF), C/ Dr. Aiguader, 80. 08003-Barcelona, Spain. jabril@imim.es', 'Spain|Spain', 0, 'Computational Biology|Genome|Sequence Analysis, DNA|Sequence Analysis, RNA|Software', 'Journal Article', '10.1093/bioinformatics/16.8.743', '11099262', 'gff2psis a program for visualizing annotations of genomic sequences. The program takes the annotated features on a genomic sequence in GFF format as input, and produces a visual output in PostScript. While it can be used in a very simple way, it also allows for a great degree of customization through a number of options and/or customization files.'),
(69806, 2000, 'bio', 'BBID: the biological biochemical image database', 'Becker, K G|White, S L|Muller, J|Engel, J', 'DNA Array Unit, RRB NCTS, National Institutes on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA. beckerk@grc.nia.nih.gov|DNA Array Unit, RRB NCTS, National Institutes on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA. beckerk@grc.nia.nih.gov|DNA Array Unit, RRB NCTS, National Institutes on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA. beckerk@grc.nia.nih.gov|DNA Array Unit, RRB NCTS, National Institutes on Aging, National Institutes of Health, 5600 Nathan Shock Drive, Baltimore, MD 21224, USA. beckerk@grc.nia.nih.gov', 'United States|United States|United States|United States', 0, 'Computer Graphics|Databases, Factual|Image Processing, Computer-Assisted', 'Journal Article', '10.1093/bioinformatics/16.8.745', '11099263', 'The Biological Biochemical Image Database is a WWW accessible relational database of archived images from research articles that describe regulatory pathways of higher eukaryotes. Pathway information is annotated and can be queried in the study of complex gene expression. In this way, complex regulatory pathways can be tested empirically in an efficient manner in the context of large-scale gene-expression systems.'),
(69807, 2000, 'bio', 'PASS: prediction of activity spectra for biologically active substances', 'Lagunin, A|Stepanchikova, A|Filimonov, D|Poroikov, V', 'Laboratory of Structure-Function Based Drug Design, Institute of Biomedical Chemistry RAMS, Moscow, Pogodinskaya str., 10, 119832, Russia. pass@ibmh.msk.su|Laboratory of Structure-Function Based Drug Design, Institute of Biomedical Chemistry RAMS, Moscow, Pogodinskaya str., 10, 119832, Russia. pass@ibmh.msk.su|Laboratory of Structure-Function Based Drug Design, Institute of Biomedical Chemistry RAMS, Moscow, Pogodinskaya str., 10, 119832, Russia. pass@ibmh.msk.su|Laboratory of Structure-Function Based Drug Design, Institute of Biomedical Chemistry RAMS, Moscow, Pogodinskaya str., 10, 119832, Russia. pass@ibmh.msk.su', '-|-|-|-', 336, 'Drug Design|Drug Evaluation, Preclinical|Internet|Software|Structure-Activity Relationship', 'Journal Article', '10.1093/bioinformatics/16.8.747', '11099264', 'The concept of the biological activity spectrum was introduced to describe the properties of biologically active substances. The PASS (prediction of activity spectra for substances) software product, which predicts more than 300 pharmacological effects and biochemical mechanisms on the basis of the structural formula of a substance, may be efficiently used to find new targets (mechanisms) for some ligands and, conversely, to reveal new ligands for some biological targets. We have developed a WWW interface for the PASS software. A WWW server for the on-line prediction of the biological activity spectra of substances has been constructed.'),
(69808, 2000, 'bio', 'ISMB-2000: bioinformatics enters a new millennium', '-', '-', '-', 0, '-', 'Journal Article', '10.1093/bioinformatics/16.9.749', '11108696', '-'),
(69809, 2000, 'bio', 'Ballast: blast post-processing based on locally conserved segments', 'Plewniak, F|Thompson, J D|Poch, O', 'Institut de Génétique et de Biologie Moléculaire et Cellulaire, Laboratoire de Biologie Structurale, (CNRS/INSERM/ULP), BP 163, 67404 Illkirch Cedex, France. plewniak@igbmc.u-strasbg.fr|Institut de Génétique et de Biologie Moléculaire et Cellulaire, Laboratoire de Biologie Structurale, (CNRS/INSERM/ULP), BP 163, 67404 Illkirch Cedex, France. plewniak@igbmc.u-strasbg.fr|Institut de Génétique et de Biologie Moléculaire et Cellulaire, Laboratoire de Biologie Structurale, (CNRS/INSERM/ULP), BP 163, 67404 Illkirch Cedex, France. plewniak@igbmc.u-strasbg.fr', 'France|France|France', 0, 'Algorithms|Amino Acid Sequence|Animals|Caenorhabditis elegans|Computational Biology|Conserved Sequence|Databases, Factual|Genomics|Haemophilus influenzae|Humans|Internet|Predictive Value of Tests|Proteins|Reproducibility of Results|Saccharomyces cerevisiae|Sequence Alignment|Sequence Homology, Amino Acid|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/16.9.750', '11108697', 'Blast programs are very efficient in finding relatively strong similarities but some very distantly related sequences are given a very high Expect value and are ranked very low in Blast results. We have developed Ballast, a program to predict local maximum segments (LMSs-i.e. sequence segments conserved relatively to their flanking regions) from a single Blast database search and to highlight these divergent homologues. The TBlastN database searches can also be processed with the help of information from a joint BlastP search.'),
(69810, 2000, 'bio', 'PHAT: a transmembrane-specific substitution matrix Predicted hydrophobic and transmembrane', 'Ng, P C|Henikoff, J G|Henikoff, S', 'Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.|Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.|Department of Bioengineering, University of Washington, Seattle, WA 98195, USA.', 'United States|United States|United States', 108, 'Algorithms|Amino Acid Sequence|Computational Biology|Consensus Sequence|Databases, Factual|Membrane Proteins|Models, Theoretical|Predictive Value of Tests|Proteins|Reproducibility of Results|Sequence Alignment|Sequence Homology, Amino Acid', 'Journal Article', '10.1093/bioinformatics/16.9.760', '11108698', 'Database searching algorithms for proteins use scoring matrices based on average protein properties, and thus are dominated by globular proteins. However, since transmembrane regions of a protein are in a distinctly different environment than globular proteins, one would expect generalized substitution matrices to be inappropriate for transmembrane regions.'),
(69811, 2000, 'bio', 'Identification of novel multi-transmembrane proteins from genomic databases using quasi-periodic structural properties', 'Kim, J|Moriyama, E N|Warr, C G|Clyne, P J|Carlson, J R', 'Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA. junhyong.kim@yale.edu|Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA. junhyong.kim@yale.edu|Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA. junhyong.kim@yale.edu|Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA. junhyong.kim@yale.edu|Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06520-8106, USA. junhyong.kim@yale.edu', 'United States|United States|United States|United States|United States', 0, 'Algorithms|Amino Acid Sequence|Animals|Computational Biology|Databases, Factual|Drosophila|Genomics|Membrane Proteins|Periodicity|Predictive Value of Tests|Receptors, Odorant|Reproducibility of Results|Sequence Alignment', 'Journal Article', '10.1093/bioinformatics/16.9.767', '11108699', 'Identification of novel G protein-coupled receptors and other multi-transmembrane proteins from genomic databases using structural features.'),
(69812, 2000, 'bio', 'MaxSub: an automated measure for the assessment of protein structure prediction quality', 'Siew, N|Elofsson, A|Rychlewski, L|Fischer, D', 'Department of Chemistry, Ben Gurion University, Beer-Sheva 84015, Israel. nomsiew@cs.bgu.ac.il|Department of Chemistry, Ben Gurion University, Beer-Sheva 84015, Israel. nomsiew@cs.bgu.ac.il|Department of Chemistry, Ben Gurion University, Beer-Sheva 84015, Israel. nomsiew@cs.bgu.ac.il|Department of Chemistry, Ben Gurion University, Beer-Sheva 84015, Israel. nomsiew@cs.bgu.ac.il', 'Israel|Israel|Israel|Israel', 305, 'Algorithms|Amino Acid Sequence|Bacterial Proteins|Computational Biology|Computer Simulation|Models, Molecular|Numerical Analysis, Computer-Assisted|Peptide Initiation Factors|Predictive Value of Tests|Protein Folding|Protein Structure, Tertiary|Reproducibility of Results|Software Validation', 'Evaluation Studies', '10.1093/bioinformatics/16.9.776', '11108700', 'Evaluating the accuracy of predicted models is critical for assessing structure prediction methods. Because this problem is not trivial, a large number of different assessment measures have been proposed by various authors, and it has already become an active subfield of research (Moult et al. (1997,1999) and CAFASP (Fischer et al. 1999) prediction experiments have demonstrated that it has been difficult to choose one single, best method to be used in the evaluation. Consequently, the CASP3 evaluation was carried out using an extensive set of especially developed numerical measures, coupled with human-expert intervention. As part of our efforts towards a higher level of automation in the structure prediction field, here we investigate the suitability of a fully automated, simple, objective, quantitative and reproducible method that can be used in the automatic assessment of models in the upcoming CAFASP2 experiment. Such a method should (a) produce one single number that measures the quality of a predicted model and (b) perform similarly to human-expert evaluations.'),
(69813, 2000, 'bio', 'Extending the method of mathematically controlled comparison to include numerical comparisons', 'Alves, R|Savageau, M A', 'Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II, Ann Arbor, MI 48109-0620, USA.|Department of Microbiology and Immunology, University of Michigan Medical School, 5641 Medical Science Building II, Ann Arbor, MI 48109-0620, USA.', 'United States|United States', 57, 'Computational Biology|Computer Simulation|Mathematical Computing|Models, Biological|Numerical Analysis, Computer-Assisted|Reproducibility of Results', 'Comparative Study', '10.1093/bioinformatics/16.9.786', '11108701', 'The method of mathematically controlled comparison has been used for some time to determine which of two alternative regulatory designs is better according to specific quantitative criteria for functional effectiveness. In some cases, the results obtained using this technique are general and independent of parameter values and the answers are clear-cut. In others, the result might be general, but the demonstration is difficult and numerical results with specific parameter values can help to clarify the situation. In either case, numerical results with specific parameter values can also provide an answer to the question of how much larger the values might be. In contrast, a more ambiguous result is obtained when either of the alternatives can have the larger value for a given systemic property, depending on the specific values of the parameters. In any case, introduction of specific values for the parameters reduces the generality of the results. Therefore, we have been motivated to develop and apply statistical methods that would permit the use of numerical values for the parameters and yet retain some of the generality that makes mathematically controlled comparison so attractive.'),
(69814, 2000, 'bio', 'Engineering support vector machine kernels that recognize translation initiation sites', 'Zien, A|Rätsch, G|Mika, S|Schölkopf, B|Lengauer, T|Müller, K R', 'GMD.SCAI, Schloss Birlinghoven, 53754 Sankt Augustin, Germany. Alexander.Zien@gmd.de|GMD.SCAI, Schloss Birlinghoven, 53754 Sankt Augustin, Germany. Alexander.Zien@gmd.de|GMD.SCAI, Schloss Birlinghoven, 53754 Sankt Augustin, Germany. Alexander.Zien@gmd.de|GMD.SCAI, Schloss Birlinghoven, 53754 Sankt Augustin, Germany. Alexander.Zien@gmd.de|GMD.SCAI, Schloss Birlinghoven, 53754 Sankt Augustin, Germany. Alexander.Zien@gmd.de|GMD.SCAI, Schloss Birlinghoven, 53754 Sankt Augustin, Germany. Alexander.Zien@gmd.de', 'Germany|Germany|Germany|Germany|Germany|Germany', 296, 'Algorithms|Animals|Codon, Initiator|Computational Biology|Databases, Factual|Genomics|Humans|Predictive Value of Tests|Protein Biosynthesis|Reproducibility of Results|Sensitivity and Specificity|Sequence Analysis, DNA|Vertebrates', 'Journal Article', '10.1093/bioinformatics/16.9.799', '11108702', 'In order to extract protein sequences from nucleotide sequences, it is an important step to recognize points at which regions start that code for proteins. These points are called translation initiation sites (TIS).'),
(69815, 2000, 'bio', 'An iterative method for faster sum-of-pairs multiple sequence alignment', 'Reinert, K|Stoye, J|Will, T', 'Celera Genomics, Informatics Research, 45 West Gude Drive, Rockville, MD 20850, USA.|Celera Genomics, Informatics Research, 45 West Gude Drive, Rockville, MD 20850, USA.|Celera Genomics, Informatics Research, 45 West Gude Drive, Rockville, MD 20850, USA.', 'United States|United States|United States', 44, 'Algorithms|Computational Biology|Conserved Sequence|Cytochrome c Group|Databases, Factual|Predictive Value of Tests|Reproducibility of Results|Sequence Alignment|Sequence Homology, Amino Acid|Time Factors', 'Journal Article', '10.1093/bioinformatics/16.9.808', '11108703', 'Multiple sequence alignment is an important tool in computational biology. In order to solve the task of computing multiple alignments in affordable time, the most commonly used multiple alignment methods have to use heuristics. Nevertheless, the computation of optimal multiple alignments is important in its own right, and it provides a means of evaluating heuristic approaches or serves as a subprocedure of heuristic alignment methods.'),
(69816, 2000, 'bio', 'BALL--rapid software prototyping in computational molecular biology Biochemicals Algorithms Library', 'Kohlbacher, O|Lenhof, H P', 'Max-Planck-Institut für Informatik, Im Stadtwald, 66123 Saarbrücken, Germany. oliver@mpi-sb.mpg.de|Max-Planck-Institut für Informatik, Im Stadtwald, 66123 Saarbrücken, Germany. oliver@mpi-sb.mpg.de', 'Germany|Germany', 82, 'Algorithms|Computational Biology|Computer Simulation|Databases, Factual|Internet|Protein Binding|Protein Structure, Tertiary|Software|Software Validation|Time Factors|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/16.9.815', '11108704', 'Rapid software prototyping can significantly reduce development times in the field of computational molecular biology and molecular modeling. Biochemical Algorithms Library (BALL) is an application framework in C++ that has been specifically designed for this purpose.'),
(69817, 2000, 'bio', 'Pathway analysis in metabolic databases via differential metabolic display (DMD)', 'Küffner, R|Zimmer, R|Lengauer, T', 'GMD-German National Research Center for Information Technology, Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany. Robert.Kueffner@gmd.de|GMD-German National Research Center for Information Technology, Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany. Robert.Kueffner@gmd.de|GMD-German National Research Center for Information Technology, Institute for Algorithms and Scientific Computing (SCAI), Schloss Birlinghoven, D-53754 Sankt Augustin, Germany. Robert.Kueffner@gmd.de', 'Germany|Germany|Germany', 99, 'Algorithms|Catalysis|Computational Biology|Computer Simulation|Data Display|Databases, Factual|Enzymes|Glycolysis|Metabolism|Mycoplasma|Yeasts', 'Journal Article', '10.1093/bioinformatics/16.9.825', '11108705', 'A number of metabolic databases are available electronically, some with features for querying and visualizing metabolic pathways and regulatory networks. We present a unifying, systematic approach based on PETRI nets for storing, displaying, comparing, searching and simulating such nets from a number of different sources.'),
(69818, 2000, 'bio', 'Detection of a surface-exposed PEST like sequence in the metabotropic glutamate receptor mGluR1 alpha', 'Soloviev, M M', 'Medical Research Council, Anatomical Neuropharmacology Unit, Oxford OX1 3TH, United Kingdom. mikhail.soloviev@pharm.ox.ac.uk', 'United Kingdom', 6, 'Amino Acid Motifs|Amino Acid Sequence|Animals|Binding Sites|Carrier Proteins|Homer Scaffolding Proteins|Neural Networks (Computer)|Neuropeptides|Protein Structure, Secondary|Rats|Receptors, Cell Surface|Receptors, Metabotropic Glutamate|Sequence Analysis, Protein|Sequence Homology, Amino Acid', 'Journal Article', '10.1093/bioinformatics/16.9.837', '11108706', '-'),
(69819, 2000, 'bio', 'Profiles from structure based sequence alignment of porins can identify beta stranded integral membrane proteins', 'Gnanasekaran, T V|Peri, S|Arockiasamy, A|Krishnaswamy, S', 'Bioinformatics Centre, School of Biotechnology, Madurai Kamaraj University, Madurai, India.|Bioinformatics Centre, School of Biotechnology, Madurai Kamaraj University, Madurai, India.|Bioinformatics Centre, School of Biotechnology, Madurai Kamaraj University, Madurai, India.|Bioinformatics Centre, School of Biotechnology, Madurai Kamaraj University, Madurai, India.', 'India|India|India|India', 29, 'Algorithms|Amino Acid Motifs|Consensus Sequence|Conserved Sequence|Databases, Factual|Membrane Proteins|Porins|Protein Structure, Secondary|Sequence Alignment|Sequence Analysis, Protein', 'Journal Article', '10.1093/bioinformatics/16.9.839', '11108707', '-'),
(69820, 2000, 'bio', 'ODNBase--a web database for antisense oligonucleotide effectiveness studies Oligodeoxynucleotides', 'Giddings, M C|Matveeva, O V|Atkins, J F|Gesteland, R F', 'Department of Human Genetics, University of Utah, SLC, UT 84112, USA. giddings@genetics.utah.edu|Department of Human Genetics, University of Utah, SLC, UT 84112, USA. giddings@genetics.utah.edu|Department of Human Genetics, University of Utah, SLC, UT 84112, USA. giddings@genetics.utah.edu|Department of Human Genetics, University of Utah, SLC, UT 84112, USA. giddings@genetics.utah.edu', 'United States|United States|United States|United States', 16, 'Animals|Databases, Factual|Drug Design|Humans|Internet|Mammals|Oligonucleotides, Antisense|RNA, Messenger|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/16.9.843', '11108708', 'ODNBase is a database of antisense oligodeoxynucleotides targeted to mammalian mRNAs that were reported in the literature. It includes the oligo sequences tested, the measured effectiveness, the RNA that was targeted, the type of measurement assay used, the oligo concentration applied, and the reference for each oligo. It provides a searchable interface by motif content, activity level, applied concentration and RNA name. Oligo lists matching search criteria can be downloaded in a spreadsheet compatible format.'),
(69821, 2000, 'bio', 'LIAN 30: detecting linkage disequilibrium in multilocus data Linkage Analysis', 'Haubold, B|Hudson, R R', 'Max-Planck-Institut für Chemische Okologie, Carl-Zeiss-Promenade 10, D-07745 Jena, Germany. haubold@ice.mpg.de|Max-Planck-Institut für Chemische Okologie, Carl-Zeiss-Promenade 10, D-07745 Jena, Germany. haubold@ice.mpg.de', 'Germany|Germany', 411, 'Chromosome Mapping|Computational Biology|Genetic Variation|Haplotypes|Linkage Disequilibrium|Models, Genetic|Monte Carlo Method|Neisseria meningitidis|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/16.9.847', '11108709', 'LIAN is a program to test the null hypothesis of linkage equilibrium for multilocus data. LIAN incorporates both a Monte Carlo method as well as a novel algebraic method to carry out the hypothesis test. The program further returns the genetic diversity of the sample and the pairwise distances between its members.'),
(69822, 2000, 'bio', 'Bioinformatics in Australia', 'Littlejohn, T', 'Max-Planck-Institut für Chemische Okologie, Carl-Zeiss-Promenade 10, D-07745 Jena, Germany. haubold@ice.mpg.de', 'Germany', 1, 'Australia|Computational Biology|Internet', 'Editorial', '10.1093/bioinformatics/16.10.849', '11120675', '-'),
(69823, 2000, 'bio', 'Bioinorganic motifs: towards functional classification of metalloproteins', 'Degtyarenko, K', 'EMBL Outstation, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK. kirill@ebi.ac.uk', 'United Kingdom', 78, 'Amino Acid Motifs|Chemical Phenomena|Chemistry, Bioinorganic|Computational Biology|Databases, Factual|Enzymes|Evolution, Molecular|Metalloproteins|Metals', 'Journal Article', '10.1093/bioinformatics/16.10.851', '11120676', 'The habitat of bioinorganic motifs (BIMs) is at the interface of biological inorganic chemistry and bioinformatics. BIM is defined as a common structural feature shared by functionally related, but not necessarily homologous, proteins, and consisting of the metal atom(s) and first coordination shell ligands. BIMs appear to be suitable for classification of metal centres at any level, from groups of unrelated proteins with similar function to different functional states of the same protein, and for description of possible evolutionary relationships of metalloproteins. However, they have not attracted wide attention from the bioinformatics community. Although their presence is appreciated, they are difficult to predict-therefore the current high-throughput initiatives are likely to miss or ignore them altogether. The protein sequence databases do not distinguish between proteins containing different prosthetic groups (unless they have different sequences) or between apo- and holoprotein. On the other hand, the protein structure databases include data on hetero compounds of various origin but these data are often inconsistent. A number of specialized databases dealing with BIMs and attempts to classify them are reviewed.'),
(69824, 2000, 'bio', 'Sequence analysis by additive scales: DNA structure for sequences and repeats of all lengths', 'Baldi, P|Baisnée, P F', 'Department of Information and Computer Science, College of Medicine, University of California, Irvine, CA 92697-3425, USA. pfbaldi@ics.uci.edu|Department of Information and Computer Science, College of Medicine, University of California, Irvine, CA 92697-3425, USA. pfbaldi@ics.uci.edu', 'United States|United States', 37, 'Animals|Computer Simulation|DNA|Dinucleotide Repeats|Humans|Models, Statistical|Nucleic Acid Conformation|Primates|Repetitive Sequences, Nucleic Acid|Sequence Analysis, DNA|Tandem Repeat Sequences|Trinucleotide Repeats', 'Journal Article', '10.1093/bioinformatics/16.10.865', '11120677', 'DNA structure plays an important role in a variety of biological processes. Different di- and tri-nucleotide scales have been proposed to capture various aspects of DNA structure including base stacking energy, propeller twist angle, protein deformability, bendability, and position preference. Yet, a general framework for the computational analysis and prediction of DNA structure is still lacking. Such a framework should in particular address the following issues: (1) construction of sequences with extremal properties, (2) quantitative evaluation of sequences with respect to a given genomic background, (3) automatic extraction of extremal sequences and profiles from genomic databases, (4) distribution and asymptotic behavior as the length N of the sequences increases, and (5) complete analysis of correlations between scales.'),
(69825, 2000, 'bio', 'Information theoretical probe selection for hybridisation experiments', 'Herwig, R|Schmitt, A O|Steinfath, M|OBrien, J|Seidel, H|Meier-Ewert, S|Lehrach, H|Radelof, U', 'Max-Planck Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany. herwig@molgen.mpg.de|Max-Planck Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany. herwig@molgen.mpg.de|Max-Planck Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany. herwig@molgen.mpg.de|Max-Planck Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany. herwig@molgen.mpg.de|Max-Planck Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany. herwig@molgen.mpg.de|Max-Planck Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany. herwig@molgen.mpg.de|Max-Planck Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany. herwig@molgen.mpg.de|Max-Planck Institut für Molekulare Genetik, Ihnestrasse 73, D-14195 Berlin, Germany. herwig@molgen.mpg.de', 'Germany|Germany|Germany|Germany|Germany|Germany|Germany|Germany', 38, 'Algorithms|Animals|DNA Fingerprinting|DNA Probes|Humans|Nucleic Acid Hybridization|Oligodeoxyribonucleotides|Rodentia', 'Journal Article', '10.1093/bioinformatics/16.10.890', '11120678', 'The choice of probes is an important feature of hybridisation experiments. In this paper we present an algorithm that optimises probes with respect to a training set of sequences based on Shannon entropy as a quality criterion. The practical motivation for our algorithm is oligonucleotide fingerprinting, a method for the simultaneous identification of sequences (cDNA or genomic DNA) by their hybridisation tags according to a set of short probes such as octamers, although the algorithm is of course not restricted to that application.'),
(69826, 2000, 'bio', 'USAGE: a web-based approach towards the analysis of SAGE data Serial Analysis of Gene Expression', 'van Kampen, A H|van Schaik, B D|Pauws, E|Michiels, E M|Ruijter, J M|Caron, H N|Versteeg, R|Heisterkamp, S H|Leunissen, J A|Baas, F|van der Mee, M', 'Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands. a.h.vancampen@amc.uva.nl|Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands. a.h.vancampen@amc.uva.nl|Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands. a.h.vancampen@amc.uva.nl|Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands. a.h.vancampen@amc.uva.nl|Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands. a.h.vancampen@amc.uva.nl|Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands. a.h.vancampen@amc.uva.nl|Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands. a.h.vancampen@amc.uva.nl|Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands. a.h.vancampen@amc.uva.nl|Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands. a.h.vancampen@amc.uva.nl|Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands. a.h.vancampen@amc.uva.nl|Bioinformatics Laboratory, Academic Medical Center, Meibergdreef 9, 1000 AZ Amsterdam, The Netherlands. a.h.vancampen@amc.uva.nl', 'Netherlands|Netherlands|Netherlands|Netherlands|Netherlands|Netherlands|Netherlands|Netherlands|Neth', 34, 'Databases, Factual|Expressed Sequence Tags|Gene Expression Profiling|Humans|Information Storage and Retrieval|Internet|RNA, Messenger|Software', 'Journal Article', '10.1093/bioinformatics/16.10.899', '11120679', 'SAGE enables the determination of genome-wide mRNA expression profiles. A comprehensive analysis of SAGE data requires software, which integrates (statistical) data analysis methods with a database system. Furthermore, to facilitate data sharing between users, the application should reside on a central server and be accessed via the internet. Since such an application was not available we developed the USAGE package.'),
(69827, 2000, 'bio', 'Support vector machine classification and validation of cancer tissue samples using microarray expression data', 'Furey, T S|Cristianini, N|Duffy, N|Bednarski, D W|Schummer, M|Haussler, D', 'Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. booch@cse.usc.edu|Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. booch@cse.usc.edu|Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. booch@cse.usc.edu|Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. booch@cse.usc.edu|Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. booch@cse.usc.edu|Department of Computer Science, University of California, Santa Cruz, Santa Cruz, CA 95064, USA. booch@cse.usc.edu', 'United States|United States|United States|United States|United States|United States', 1736, 'Acute Disease|Algorithms|Artificial Intelligence|Colonic Neoplasms|DNA, Neoplasm|Databases, Factual|Female|Humans|Leukemia, Myeloid|Oligonucleotide Array Sequence Analysis|Ovarian Neoplasms|Ovary|Precursor Cell Lymphoblastic Leukemia-Lymphoma|Software', 'Evaluation Studies', '10.1093/bioinformatics/16.10.906', '11120680', 'DNA microarray experiments generating thousands of gene expression measurements, are being used to gather information from tissue and cell samples regarding gene expression differences that will be useful in diagnosing disease. We have developed a new method to analyse this kind of data using support vector machines (SVMs). This analysis consists of both classification of the tissue samples, and an exploration of the data for mis-labeled or questionable tissue results.'),
(69828, 2000, 'bio', 'CAST: an iterative algorithm for the complexity analysis of sequence tracts Complexity analysis of sequence tracts', 'Promponas, V J|Enright, A J|Tsoka, S|Kreil, D P|Leroy, C|Hamodrakas, S|Sander, C|Ouzounis, C A', 'Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens GR-15701, Greece.|Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens GR-15701, Greece.|Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens GR-15701, Greece.|Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens GR-15701, Greece.|Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens GR-15701, Greece.|Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens GR-15701, Greece.|Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens GR-15701, Greece.|Department of Cell Biology and Biophysics, Faculty of Biology, University of Athens, Athens GR-15701, Greece.', 'Greece|Greece|Greece|Greece|Greece|Greece|Greece|Greece', 112, 'Algorithms|Animals|DNA, Protozoan|Databases, Factual|Genes, Protozoan|Open Reading Frames|Plasmodium falciparum|Sequence Analysis, DNA', 'Journal Article', '10.1093/bioinformatics/16.10.915', '11120681', 'Sensitive detection and masking of low-complexity regions in protein sequences. Filtered sequences can be used in sequence comparison without the risk of matching compositionally biased regions. The main advantage of the method over similar approaches is the selective masking of single residue types without affecting other, possibly important, regions.'),
(69829, 2000, 'bio', 'The reduction of large molecular profiles to informative components using a genetic algorithm', 'Stefanini, F M|Camussi, A', 'Department of Statistics G.Parenti, University of Florence, Viale Morgagni 59, 50134, Firenze, Italy. stefani@ds.unifi.it|Department of Statistics G.Parenti, University of Florence, Viale Morgagni 59, 50134, Firenze, Italy. stefani@ds.unifi.it', 'Italy|Italy', 8, 'Algorithms|Computer Simulation|DNA Fingerprinting|Genetic Markers|Humans|Pilot Projects', 'Journal Article', '10.1093/bioinformatics/16.10.923', '11120682', 'Molecular profiles (DNA fingerprints) may be used to allocate an individual of unknown membership to one among the known groups of a reference population. Time and costs of profile assessment may be reduced by identifying informative profile components (markers).'),
(69830, 2000, 'bio', 'Finding pathogenicity islands and gene transfer events in genome data', 'Liò, P|Vannucci, M', 'Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK. p.lio@zoo.cam.ac.uk|Department of Zoology, University of Cambridge, Downing Street, Cambridge CB2 3EH, UK. p.lio@zoo.cam.ac.uk', 'United Kingdom|United Kingdom', 57, 'Base Composition|Base Sequence|DNA, Bacterial|Data Interpretation, Statistical|Databases, Factual|GC Rich Sequence|Gene Transfer, Horizontal|Genome, Bacterial|Helicobacter pylori|Models, Genetic|Models, Statistical|Neisseria meningitidis|Numerical Analysis, Computer-Assisted|Sequence Analysis, DNA', 'Journal Article', '10.1093/bioinformatics/16.10.932', '11120683', 'There is a growing literature on wavelet theory and wavelet methods showing improvements on more classical techniques, especially in the contexts of smoothing and extraction of fundamental components of signals. G+C patterns occur at different lengths (scales) and, for this reason, G+C plots are usually difficult to interpret. Current methods for genome analysis choose a window size and compute a chi(2) statistics of the average value for each window with respect to the whole genome.'),
(69831, 2000, 'bio', 'Matching amino acid and nucleotide sequences of mouse rheumatoid factor CDRH3-FRH4 segments to other mouse antibodies with known specificities', 'Johnson, G|Wu, T T', 'Department of Biochemistry, Northwestern University, Evanston, IL 60208, USA.|Department of Biochemistry, Northwestern University, Evanston, IL 60208, USA.', 'United States|United States', 0, 'Amino Acid Sequence|Amino Acids|Animals|Antibody Specificity|Autoantibodies|Complementarity Determining Regions|Databases, Factual|Immunoglobulin Heavy Chains|Immunoglobulin Variable Region|Mice|Molecular Sequence Data|Nucleotides|Rheumatoid Factor|Sequence Alignment|Sequence Analysis, DNA|Sequence Analysis, Protein', 'Journal Article', '10.1093/bioinformatics/16.10.941', '11120684', '-'),
(69832, 2000, 'bio', 'Artemis: sequence visualization and annotation', 'Rutherford, K|Parkhill, J|Crook, J|Horsnell, T|Rice, P|Rajandream, M A|Barrell, B', 'The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. kmr@sanger.ac.uk|The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. kmr@sanger.ac.uk|The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. kmr@sanger.ac.uk|The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. kmr@sanger.ac.uk|The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. kmr@sanger.ac.uk|The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. kmr@sanger.ac.uk|The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK. kmr@sanger.ac.uk', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom', 2282, 'Databases, Factual|Image Processing, Computer-Assisted|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/16.10.944', '11120685', 'Artemis is a DNA sequence visualization and annotation tool that allows the results of any analysis or sets of analyses to be viewed in the context of the sequence and its six-frame translation. Artemis is especially useful in analysing the compact genomes of bacteria, archaea and lower eukaryotes, and will cope with sequences of any size from small genes to whole genomes. It is implemented in Java, and can be run on any suitable platform. Sequences and annotation can be read and written directly in EMBL, GenBank and GFF format. AVAILABITLTY: Artemis is available under the GNU General Public License from http://www.sanger.ac.uk/Software/Artemis'),
(69833, 2000, 'bio', 'MAD: a suite of tools for microarray data management and processing', 'Liao, B|Hale, W|Epstein, C B|Butow, R A|Garner, H R', 'Center for Biomedical Inventions, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.|Center for Biomedical Inventions, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.|Center for Biomedical Inventions, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.|Center for Biomedical Inventions, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.|Center for Biomedical Inventions, University of Texas Southwestern Medical Center at Dallas, 5323 Harry Hines Blvd, Dallas, TX 75390, USA.', 'United States|United States|United States|United States|United States', 8, 'Databases, Factual|Electronic Data Processing|Oligonucleotide Array Sequence Analysis|Software', 'Journal Article', '10.1093/bioinformatics/16.10.946', '11120686', 'Microarray data management and processing (MAD) is a set of Windows integrated software for microarray analysis. It consists of a relational database for data storage with many user-interfaces for data manipulation, several text file parsers and Microsoft Excel macros for automation of data processing, and a generator to produce text files that are ready for cluster analysis.'),
(69834, 2000, 'bio', 'A space-efficient algorithm for aligning large genomic sequences', 'Morgenstern, B', 'MIPS-Max-Planck-Institut für Biochemic, Am Klopferspitz 18a, 82152 Martinsried, Germany. morgenstern@mips.biochem.mpg.de', 'Germany', 25, 'Algorithms|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/16.10.948', '11120687', 'In the segment-by-segment approach to sequence alignment, pairwise and multiple alignments are generated by comparing gap-free segments of the sequences under study. This method is particularly efficient in detecting local homologies, and it has been used to identify functional regions in large genomic sequences. Herein, an algorithm is outlined that calculates optimal pairwise segment-by-segment alignments in essentially linear space. AVAILABILTIY: The program is available at the Bielefeld Bioinformatics Server (BiBiServ) at http://bibiserv.techfak. uni-bielefeld.de/dialign/'),
(69835, 2000, 'bio', 'MASIA: recognition of common patterns and properties in multiple aligned protein sequences', 'Zhu, H|Schein, C H|Braun, W', 'Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555-1157, USA.|Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555-1157, USA.|Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX 77555-1157, USA.', 'United States|United States|United States', 0, 'Sequence Alignment|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/16.10.950', '11120688', 'MASIA is a software tool for pattern recognition in multiple aligned protein sequences. MASIA converts a sequence to a properties matrix that can be scanned in both vertical and horizontal steps. Consistent patterns are recognized based on the statistical significance of their occurrence. Preset macros can be altered on-line to seek any combination of amino acid properties or sequence characteristics. MASIA output can be used directly by our programs to predict the 3D structure of proteins.'),
(69836, 2000, 'bio', 'POWER_SAGE: comparing statistical tests for SAGE experiments', 'Man, M Z|Wang, X|Wang, Y', 'Biostatisties, PGRD, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. michael.man@pfizer.com|Biostatisties, PGRD, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. michael.man@pfizer.com|Biostatisties, PGRD, 2800 Plymouth Road, Ann Arbor, MI 48105, USA. michael.man@pfizer.com', 'United States|United States|United States', 129, 'Algorithms|Chi-Square Distribution|Computational Biology|Expressed Sequence Tags|Gene Expression Profiling|Monte Carlo Method|RNA, Messenger|Software', 'Comparative Study', '10.1093/bioinformatics/16.11.953', '11159306', 'The Serial Analysis of Gene Expression (SAGE) technology determines the expression level of a gene by measuring the frequency of a sequence tag derived from the corresponding mRNA transcript. Several statistical tests have been developed to detect significant differences in tag frequency between two samples. However, which one of these tests has the greatest power to detect real changes remains undetermined.'),
(69837, 2000, 'bio', 'Prediction whether a human cDNA sequence contains initiation codon by combining statistical information and similarity with protein sequences', 'Nishikawa, T|Ota, T|Isogai, T', 'Helix Research Institute, Chiba, Japan. nisikawa@crl.hitachi.co.jp|Helix Research Institute, Chiba, Japan. nisikawa@crl.hitachi.co.jp|Helix Research Institute, Chiba, Japan. nisikawa@crl.hitachi.co.jp', 'Japan|Japan|Japan', 0, 'Amino Acid Sequence|Codon, Initiator|Computational Biology|DNA, Complementary|Humans|Molecular Sequence Data|Proteins|Sequence Homology, Amino Acid|Software|Software Design', 'Evaluation Studies', '10.1093/bioinformatics/16.11.960', '11159307', 'In the previous works, we developed ATGpr, a computer program for predicting the fullness of a cDNA, i.e. whether it contains an initiation codon or not. Statistical information of short nucleotide fragments was fully exploited in the prediction algorithm. However, sequence similarities to known proteins, which are becoming increasingly available due to recent rapid growth of protein database, were not used in the prediction. In this work, we present a new prediction algorithm based on both statistical and similarity information, which provides better performance in sensitivity and specificity.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(69838, 2000, 'bio', 'Short interrupted palindromes on the extragenic DNA of Escherichia coli K-12, Haemophilus influenzae and Neisseria meningitidis', 'Vasconcelos, A T|Maia, M A|de Almeida, D F', 'Laboratório Nacional de Computação Científica, MCT, Petrópolis, RJ, 25651-070, Brazil. atrv@lncc.br|Laboratório Nacional de Computação Científica, MCT, Petrópolis, RJ, 25651-070, Brazil. atrv@lncc.br|Laboratório Nacional de Computação Científica, MCT, Petrópolis, RJ, 25651-070, Brazil. atrv@lncc.br', 'Brazil|Brazil|Brazil', 6, 'Computational Biology|DNA, Bacterial|Escherichia coli|Genetic Techniques|Genome, Bacterial|Haemophilus influenzae|Neisseria meningitidis|Regression Analysis|Repetitive Sequences, Nucleic Acid', 'Comparative Study', '10.1093/bioinformatics/16.11.968', '11159308', 'The importance of the various kinds of repetitive nucleotide sequences for the workings of bacterial DNA has been widely recognized. This work is concerned with the distribution of a particular group of repetitive sequences, the short-sequenced interrupted extragenic palindromes, on the genetic maps of Escherichia coli K-12, Haemophilus influenzae Rd and Neisseria meningitidis Z2491 and MC58. A tool has been developed based upon a statistical hypothesis test taking into account the markovian structure of random sequences in order to determine the non-random character of extragenic palindromes.'),
(69839, 2000, 'bio', 'Estimating the significance of sequence order in protein secondary structure and prediction', 'Park, J|Dietmann, S|Heger, A|Holm, L', 'The European Bioinformatics Institute, EMBL Outstation, Cambridge CB10 1SD, UK. jong@biosophy.org|The European Bioinformatics Institute, EMBL Outstation, Cambridge CB10 1SD, UK. jong@biosophy.org|The European Bioinformatics Institute, EMBL Outstation, Cambridge CB10 1SD, UK. jong@biosophy.org|The European Bioinformatics Institute, EMBL Outstation, Cambridge CB10 1SD, UK. jong@biosophy.org', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom', 8, 'Algorithms|Amino Acid Sequence|Computational Biology|Databases, Factual|Molecular Sequence Data|Protein Structure, Secondary|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/16.11.978', '11159309', 'How critical is the sequence order information in predicting protein secondary structure segments? We tried to get a rough insight on it from a theoretical approach using both a prediction algorithm and structural fragments from Protein Databank (PDB).'),
(69840, 2000, 'bio', 'Iterative sequence/secondary structure search for protein homologs: comparison with amino acid sequence alignments and application to fold recognition in genome databases', 'Wallqvist, A|Fukunishi, Y|Murphy, L R|Fadel, A|Levy, R M', 'Department of Chemistry, Rutgers University, Wright-Rieman Laboratories, 610 Taylor Rd, Piscataway, NJ 08854-8087, USA. anders@rutchem.rutgers.edu|Department of Chemistry, Rutgers University, Wright-Rieman Laboratories, 610 Taylor Rd, Piscataway, NJ 08854-8087, USA. anders@rutchem.rutgers.edu|Department of Chemistry, Rutgers University, Wright-Rieman Laboratories, 610 Taylor Rd, Piscataway, NJ 08854-8087, USA. anders@rutchem.rutgers.edu|Department of Chemistry, Rutgers University, Wright-Rieman Laboratories, 610 Taylor Rd, Piscataway, NJ 08854-8087, USA. anders@rutchem.rutgers.edu|Department of Chemistry, Rutgers University, Wright-Rieman Laboratories, 610 Taylor Rd, Piscataway, NJ 08854-8087, USA. anders@rutchem.rutgers.edu', 'United States|United States|United States|United States|United States', 6, 'Algorithms|Amino Acid Sequence|Animals|Computational Biology|Databases, Factual|Genome|Hemoglobins|Models, Molecular|Molecular Sequence Data|Protein Folding|Protein Structure, Secondary|Proteins|Sequence Alignment|Software', 'Comparative Study', '10.1093/bioinformatics/16.11.988', '11159310', 'Sequence alignment techniques have been developed into extremely powerful tools for identifying the folding families and function of proteins in newly sequenced genomes. For a sufficiently low sequence identity it is necessary to incorporate additional structural information to positively detect homologous proteins. We have carried out an extensive analysis of the effectiveness of incorporating secondary structure information directly into the alignments for fold recognition and identification of distant protein homologs. A secondary structure similarity matrix based on a database of three-dimensionally aligned proteins was first constructed. An iterative application of dynamic programming was used which incorporates linear combinations of amino acid and secondary structure sequence similarity scores. Initially, only primary sequence information is used. Subsequently contributions from secondary structure are phased in and new homologous proteins are positively identified if their scores are consistent with the predetermined error rate.'),
(69841, 2000, 'bio', 'Arbor 3D: an interactive environment for examining phylogenetic and taxonomic trees in multiple dimensions', 'Ruths, D A|Chen, E S|Ellis, L', 'Rice University, HiPerSoft, MS-41, 6100 S. Main, Houston, Texas 77005, USA. druths@rice.edu|Rice University, HiPerSoft, MS-41, 6100 S. Main, Houston, Texas 77005, USA. druths@rice.edu|Rice University, HiPerSoft, MS-41, 6100 S. Main, Houston, Texas 77005, USA. druths@rice.edu', 'United States|United States|United States', 14, 'Classification|Computational Biology|Computer Graphics|Computers|Databases, Factual|Genome|Phylogeny|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/16.11.1003', '11159311', 'This paper examines a new technique for the visualization of and the interaction with trees, objects frequently used to convey hierarchical relationships in biological data. Motivated by the quality of 2D tree interaction, we adapt the planar tree-of-life metaphor to a virtual, semi-immersive 3D environment. A 3D environment extends the utility of this metaphor by allowing the user to view an entire data set in a single screen. Interrogation of the tree is implemented using 3D input devices. This real-time interrogation of the tree itself provides a quick means by which to qualitatively analyse the hierarchical data. In this paper, we describe the techniques underlying the implementation of such an environment. We conclude by considering the utility of tree metaphors as a basis for the representation of highly dimensional data sets.'),
(69842, 2000, 'bio', 'Fels-Rand: an Xlisp-Stat program for the comparative analysis of data under phylogenetic uncertainty', 'Blomberg, S', 'Department of Zoology, University of Aberdeen, Aberdeen AB24 2TZ, Scotland, UK. s.blomberg@abdn.ac.uk', 'United Kingdom', 4, 'Algorithms|Computational Biology|Computer Graphics|Data Interpretation, Statistical|Genetic Techniques|Phylogeny|Random Allocation|Software', 'Comparative Study', '10.1093/bioinformatics/16.11.1010', '11159312', 'Currently available programs for the comparative analysis of phylogenetic data do not perform optimally when the phylogeny is not completely specified (i.e. the phylogeny contains polytomies). Recent literature suggests that a better way to analyse the data would be to create random trees from the known phylogeny that are fully-resolved but consistent with the known tree. A computer program is presented, Fels-Rand, that performs such analyses. A randomisation procedure is used to generate trees that are fully resolved but whose structure is consistent with the original tree. Statistics are then calculated on a large number of these randomly-generated trees. Fels-Rand uses the object-oriented features of Xlisp-Stat to manipulate internal tree representations. Xlisp-Stats dynamic graphing features are used to provide heuristic tools to aid in analysis, particularly outlier analysis. The usefulness of Xlisp-Stat as a system for phylogenetic computation is discussed.'),
(69843, 2000, 'bio', 'Processing and quality control of DNA array hybridization data', 'Beissbarth, T|Fellenberg, K|Brors, B|Arribas-Prat, R|Boer, J|Hauser, N C|Scheideler, M|Hoheisel, J D|Schütz, G|Poustka, A|Vingron, M', 'Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany.|Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany.|Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany.|Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany.|Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany.|Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany.|Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany.|Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany.|Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany.|Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany.|Abt. Theoretische Bioinformatik, Deutsches Krebsforschungszentrum, INF 280, D-69120 Heidelberg, Germany.', 'Germany|Germany|Germany|Germany|Germany|Germany|Germany|Germany|Germany|Germany|Germany', 108, 'Animals|Computational Biology|Data Interpretation, Statistical|Databases, Factual|Expressed Sequence Tags|Gene Expression Profiling|Mice|Oligonucleotide Array Sequence Analysis|Quality Control', 'Comparative Study', '10.1093/bioinformatics/16.11.1014', '11159313', 'The technology of hybridization to DNA arrays is used to obtain the expression levels of many different genes simultaneously. It enables searching for genes that are expressed specifically under certain conditions. However, the technology produces large amounts of data demanding computational methods for their analysis. It is necessary to find ways to compare data from different experiments and to consider the quality and reproducibility of the data.'),
(69844, 2000, 'bio', 'Biochemical systems analysis of genome-wide expression data', 'Voit, E O|Radivoyevitch, T', 'Department of Biometry and Epidemiology, 135 Rutledge Avenue, Medical University of South Carolina, Charleston, SC 29425, USA. VoitEO@MUSC.edu|Department of Biometry and Epidemiology, 135 Rutledge Avenue, Medical University of South Carolina, Charleston, SC 29425, USA. VoitEO@MUSC.edu', 'United States|United States', 0, 'Computational Biology|Data Interpretation, Statistical|Databases, Factual|Gene Expression Profiling|Genome, Fungal|Glycolysis|Heat-Shock Response|Models, Biological|Saccharomyces cerevisiae|Systems Analysis', 'Journal Article', '10.1093/bioinformatics/16.11.1023', '11159314', 'Modern methods of genomics have produced an unprecedented amount of raw data. The interpretation and explanation of these data constitute a major, well-recognized challenge.'),
(69845, 2000, 'bio', 'DRAGON: Database Referencing of Array Genes Online', 'Bouton, C M|Pevsner, J', 'Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA. cbouton@jhmi.edu|Department of Neuroscience, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA. cbouton@jhmi.edu', 'United States|United States', 30, 'Computational Biology|Databases, Factual|Gene Expression Profiling|Internet|Oligonucleotide Array Sequence Analysis|Online Systems', 'Journal Article', '10.1093/bioinformatics/16.11.1038', '11159315', 'Database Referencing of Array Genes ONline or DRAGON is a web-accessible database that aids in the analysis of differential gene expression data as a biological annotation tool. Users of DRAGON can submit data sets containing large lists of genes and then choose particular characteristics that DRAGON supplies for all genes on the list rapidly and simultaneously.'),
(69846, 2000, 'bio', 'MaskerAid: a performance enhancement to RepeatMasker', 'Bedell, J A|Korf, I|Gish, W', 'Genome Sequencing Center and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA.|Genome Sequencing Center and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA.|Genome Sequencing Center and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108, USA.', 'United States|United States|United States', 128, 'Animals|Computational Biology|Databases, Factual|Humans|Long Interspersed Nucleotide Elements|Repetitive Sequences, Nucleic Acid|Sequence Alignment|Short Interspersed Nucleotide Elements|Software', 'Comparative Study', '10.1093/bioinformatics/16.11.1040', '11159316', 'Identifying and masking repetitive elements is usually the first step when analyzing vertebrate genomic sequence. Current repeat identification software is sensitive but slow, creating a costly bottleneck in large-scale analyses. We have developed MaskerAid, a software enhancement to RepeatMasker that increased the speed of masking more than 30-fold at the most sensitive setting.'),
(69847, 2000, 'bio', 'Circles: automating the comparative analysis of RNA secondary structure', 'Page, R D', 'Division of Environmental and Evolutionary Biology, Institute of Biomedical and Life Sciences, Graham Kerr Building, University of Glasgow, Glasgow G12 8QQ, UK. r.page@bio.gla.ac.uk', 'United Kingdom', 4, 'Base Sequence|Computational Biology|Computer Graphics|Nucleic Acid Conformation|RNA|Sequence Homology, Nucleic Acid|Software|User-Computer Interface', 'Comparative Study', '10.1093/bioinformatics/16.11.1042', '11159317', 'Circles is a program for inferring RNA secondary structure using maximum weight matching. The program can read in an alignment in FASTA, ClustalW, or NEXUS format, compute a maximum weight matching, and export one or more secondary structures in various file formats.'),
(69848, 2000, 'bio', 'VISTA : visualizing global DNA sequence alignments of arbitrary length', 'Mayor, C|Brudno, M|Schwartz, J R|Poliakov, A|Rubin, E M|Frazer, K A|Pachter, L S|Dubchak, I', 'National Energy Research Scientific Computing Center Genome Sciences Department, Berkeley, CA 94720, USA. vista@lbl.gov|National Energy Research Scientific Computing Center Genome Sciences Department, Berkeley, CA 94720, USA. vista@lbl.gov|National Energy Research Scientific Computing Center Genome Sciences Department, Berkeley, CA 94720, USA. vista@lbl.gov|National Energy Research Scientific Computing Center Genome Sciences Department, Berkeley, CA 94720, USA. vista@lbl.gov|National Energy Research Scientific Computing Center Genome Sciences Department, Berkeley, CA 94720, USA. vista@lbl.gov|National Energy Research Scientific Computing Center Genome Sciences Department, Berkeley, CA 94720, USA. vista@lbl.gov|National Energy Research Scientific Computing Center Genome Sciences Department, Berkeley, CA 94720, USA. vista@lbl.gov|National Energy Research Scientific Computing Center Genome Sciences Department, Berkeley, CA 94720, USA. vista@lbl.gov', 'United States|United States|United States|United States|United States|United States|United States|United States', 690, 'Animals|Computational Biology|DNA|Humans|Internet|Mice|Rabbits|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/16.11.1046', '11159318', 'VISTA is a program for visualizing global DNA sequence alignments of arbitrary length. It has a clean output, allowing for easy identification of similarity, and is easily configurable, enabling the visualization of alignments of various lengths at different levels of resolution. It is currently available on the web, thus allowing for easy access by all researchers.'),
(69849, 2000, 'bio', 'VARSPLIC: alternatively-spliced protein sequences derived from SWISS-PROT and TrEMBL', 'Kersey, P|Hermjakob, H|Apweiler, R', 'EMBL Outstation Hinxton, The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK. pkersey@ebi.ac.uk|EMBL Outstation Hinxton, The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK. pkersey@ebi.ac.uk|EMBL Outstation Hinxton, The European Bioinformatics Institute (EBI), Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK. pkersey@ebi.ac.uk', 'United Kingdom|United Kingdom|United Kingdom', 0, 'Alternative Splicing|Animals|Computational Biology|Databases, Factual|Humans|Internet|Protein Isoforms|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/16.11.1048', '11159319', 'The program varsplic.pl uses information present in the SWISS-PROT and TrEMBL databases to create new records for alternatively spliced isoforms. These new records can be used in similarity searches.'),
(69850, 2000, 'bio', 'T(E)Xtopo: shaded membrane protein topology plots in LAT(E)X2epsilon', 'Beitz, E', 'Faculty of Chemistry and Pharmacy, University of Tübingen, Morgenstelle 8, 72076 Tübingen, Germany. eric.beitz@uni-tuebingen.de', 'Germany', 0, 'Amino Acid Sequence|Aquaporin 1|Aquaporins|Blood Group Antigens|Computational Biology|Databases, Factual|Humans|Internet|Membrane Proteins|Molecular Sequence Data|Protein Conformation|Software', 'Journal Article', '10.1093/bioinformatics/16.11.1050', '11159320', 'T(E)Xtopo is a LAT(E)X2epsilon macro package for plotting topology data directly from PHD predictions or SwissProt database files in publication-ready quality. The plot can be shaded automatically to emphasize conserved residues or functional properties of the residue sidechains. The addition of rich decorations, such as labels, annotations and legends, is easily accomplished.'),
(69851, 2000, 'bio', 'MPBLAST : improved BLAST performance with multiplexed queries', 'Korf, I|Gish, W', 'Genome Sequencing Center and Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA. ikorf@watson.wustl.edu|Genome Sequencing Center and Department of Genetics, Washington University School of Medicine, St Louis, MO 63108, USA. ikorf@watson.wustl.edu', 'United States|United States', 19, 'Computational Biology|Databases, Factual|Expressed Sequence Tags|Internet|Sequence Analysis|Software', 'Comparative Study', '10.1093/bioinformatics/16.11.1052', '11159321', 'We have developed a program, MPBLAST, that increases the throughput of batch BLASTN searches by multiplexing (concatenating) query sequences and thereby reducing the number of actual database searches performed. Throughput was observed to increase in reciprocal proportion to the component sequence length. For sequencing read-sized queries of 500 bp, an order of magnitude speed-up was seen.'),
(69852, 2000, 'bio', 'BLAST Search Updater: a notification system for new database matches', 'Boone, M|Upton, C', 'Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055, Victoria, BC V8W 3P6, Canada.|Department of Biochemistry and Microbiology, University of Victoria, PO Box 3055, Victoria, BC V8W 3P6, Canada.', 'Canada|Canada', 6, 'Computational Biology|DNA|Databases, Factual|Proteins|Sequence Alignment|Software|Software Design', 'Journal Article', '10.1093/bioinformatics/16.11.1054', '11159322', 'BLAST Search Updater (BSU) can help molecular biologists perform large numbers of BLAST searches routinely and screen the results for novel matches. The search result files (HTML format) and delta files (novel matches) are WWW viewable and BSU also emails users alignments of new matches.'),
(69853, 2000, 'bio', 'PhyloDraw: a phylogenetic tree drawing system', 'Choi, J H|Jung, H Y|Kim, H S|Cho, H G', 'Department of Computer Science, Pusan National University, Pusan, Korea. jhchoi@pearl.cs.pusan.ac.kr|Department of Computer Science, Pusan National University, Pusan, Korea. jhchoi@pearl.cs.pusan.ac.kr|Department of Computer Science, Pusan National University, Pusan, Korea. jhchoi@pearl.cs.pusan.ac.kr|Department of Computer Science, Pusan National University, Pusan, Korea. jhchoi@pearl.cs.pusan.ac.kr', '-|-|-|-', 0, 'Computational Biology|Computer Graphics|Internet|Phylogeny|Sequence Alignment|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/16.11.1056', '11159323', 'PhyloDraw is a unified viewing tool for phylogenetic trees. PhyloDraw supports various kinds of multi-alignment formats (Dialign2, Clustal-W, Phylip format, NEXUS, MEGA, and pairwise distance matrix) and visualizes various kinds of tree diagrams, e.g. rectangular cladogram, slanted cladogram, phylogram, unrooted tree, and radial tree. By using several control parameters, users can easily and interactively manipulate the shape of phylogenetic trees. This program can export the final tree layout to BMP (bitmap image format) and PostScript.'),
(69854, 2000, 'bio', 'The need for a human gene index', 'Jongeneel, C V', 'Department of Computer Science, Pusan National University, Pusan, Korea. jhchoi@pearl.cs.pusan.ac.kr', '-', 0, 'Abstracting and Indexing as Topic|Cluster Analysis|Computational Biology|Databases, Factual|Expressed Sequence Tags|Genome, Human|Humans|Internet|Terminology as Topic', 'Editorial', '10.1093/bioinformatics/16.12.1059', '11159324', '-'),
(69855, 2000, 'bio', 'Neural network schemes for detecting rare events in human genomic DNA', 'Choe, W|Ersoy, O K|Bina, M', 'School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA. wooyoung@ecn.purdue.edu|School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA. wooyoung@ecn.purdue.edu|School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA. wooyoung@ecn.purdue.edu', 'United States|United States|United States', 27, 'Algorithms|Alu Elements|Computational Biology|DNA|Databases, Factual|Genome, Human|Humans|Neural Networks (Computer)|Sequence Analysis, DNA', 'Journal Article', '10.1093/bioinformatics/16.12.1062', '11159325', 'Many problems in molecular biology as well as other areas involve detection of rare events in unbalanced data. We develop two sample stratification schemes in conjunction with neural networks for rare event detection in such databases. Sample stratification is a technique for making each class in a sample have equal influence on decision making. The first scheme proposed stratifies a sample by adding up the weighted sum of the derivatives during the backward pass of training. The second scheme proposed uses a technique of modified bootstrap aggregating. After training neural networks with multiple sets of bootstrapped examples of the rare event classes and subsampled examples of common event classes, multiple voting for classification is performed.'),
(69856, 2000, 'bio', 'Frequency-domain analysis of biomolecular sequences', 'Anastassiou, D', 'Department of Electrical Engineering, Columbia University, 500 West 120th Street, Mail Code 4712, New York, NY 10027, USA. anastas@ee.columbia.edu', 'United States', 31, 'Algorithms|Computational Biology|Computer Graphics|DNA|DNA, Fungal|Fourier Analysis|Proteins|Reading Frames|Saccharomyces cerevisiae|Sequence Analysis|Sequence Analysis, DNA|Signal Processing, Computer-Assisted|Software', 'Comparative Study', '10.1093/bioinformatics/16.12.1073', '11159326', 'Frequency-domain analysis of biomolecular sequences is hindered by their representation as strings of characters. If numerical values are assigned to each of these characters, then the resulting numerical sequences are readily amenable to digital signal processing.'),
(69857, 2000, 'bio', 'Optimizing reduced-space sequence analysis', 'Wheeler, R|Hughey, R', 'Department of Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA.|Department of Computer Engineering, Jack Baskin School of Engineering, University of California, Santa Cruz, CA 95064, USA.', 'United States|United States', 8, 'Algorithms|Computational Biology|Internet|Markov Chains|Sequence Alignment|Sequence Analysis|Software', 'Comparative Study', '10.1093/bioinformatics/16.12.1082', '11159327', 'Dynamic programming is the core algorithm of sequence comparison, alignment and linear hidden Markov model (HMM) training. For a pair of sequence lengths m and n, the problem can be solved readily in O(mn)time and O(mn)space. The checkpoint algorithm introduced by Grice et al. (CABIOS, 13, 45--53, 1997) runs in O(Lmn)time and O(Lm(L) square root of n)space, where L is a positive integer determined by m, n, and the amount of available workspace. The algorithm is appropriate for many string comparison problems, including all-paths and single-best-path hidden Markov model training, and is readily parallelizable. The checkpoint algorithm has a diagonal version that can solve the single-best-path alignment problem in O(mn)time and O(m + n)space.'),
(69858, 2000, 'bio', 'Protein domain decomposition using a graph-theoretic approach', 'Xu, Y|Xu, D|Gabow, H N|Gabow, H', 'Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830-6480, USA. xyn@ornl.gov|Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830-6480, USA. xyn@ornl.gov|Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830-6480, USA. xyn@ornl.gov|Computational Biosciences Section, Life Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN 37830-6480, USA. xyn@ornl.gov', 'United States|United States|United States|United States', 82, 'Algorithms|Computational Biology|Computer Graphics|Databases, Factual|Models, Molecular|Protein Structure, Tertiary|Software', 'Journal Article', '10.1093/bioinformatics/16.12.1091', '11159328', 'Automatic decomposition of a multi-domain protein into individual domains represents a highly interesting and unsolved problem. As the number of protein structures in PDB is growing at an exponential rate, there is clearly a need for more reliable and efficient methods for protein domain decomposition simply to keep the domain databases up-to-date.'),
(69859, 2000, 'bio', 'Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology', 'Li, W|Pio, F|Pawxc5x82owski, K|Godzik, A', 'San Diego Supercomputer Center, La Jolla, CA 92093, USA. liwz@sdsc.edu|San Diego Supercomputer Center, La Jolla, CA 92093, USA. liwz@sdsc.edu|San Diego Supercomputer Center, La Jolla, CA 92093, USA. liwz@sdsc.edu|San Diego Supercomputer Center, La Jolla, CA 92093, USA. liwz@sdsc.edu', 'United States|United States|United States|United States', 51, 'Algorithms|Amino Acid Sequence|Computational Biology|Computer Graphics|Database Management Systems|Databases, Factual|Molecular Sequence Data|Proteins|Sequence Alignment|Software|Software Design|User-Computer Interface', 'Comparative Study', '10.1093/bioinformatics/16.12.1105', '11159329', 'Two proteins can have a similar 3-dimensional structure and biological function, but have sequences sufficiently different that traditional protein sequence comparison algorithms do not identify their relationship. The desire to identify such relations has led to the development of more sensitive sequence alignment strategies. One such strategy is the Intermediate Sequence Search (ISS), which connects two proteins through one or more intermediate sequences. In its brute-force implementation, ISS is a strategy that repetitively uses the results of the previous query as new search seeds, making it time-consuming and difficult to analyze.'),
(69860, 2000, 'bio', 'Analysis of conservation and substitutions of secondary structure elements within protein superfamilies', 'Mizuguchi, K|Blundell, T', 'Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrookes Site, Cambridge CB2 1GA, UK. kenji@cryst.bioc.cam.ac.uk|Department of Biochemistry, University of Cambridge, 80 Tennis Court Road, Old Addenbrookes Site, Cambridge CB2 1GA, UK. kenji@cryst.bioc.cam.ac.uk', 'United Kingdom|United Kingdom', 15, 'Algorithms|Amino Acid Sequence|Amino Acid Substitution|Computational Biology|Conserved Sequence|Databases, Factual|Internet|Models, Molecular|Molecular Sequence Data|Protein Structure, Secondary|Proteins|Sequence Alignment', 'Comparative Study', '10.1093/bioinformatics/16.12.1111', '11159330', 'Structural alignments of superfamily members often exhibit insertions and deletions of secondary structure elements (SSEs), yet conserved subsets of SSEs appear to be important for maintaining the fold and facilitating common functionalities.'),
(69861, 2000, 'bio', 'A knowledge model for analysis and simulation of regulatory networks', 'Rzhetsky, A|Koike, T|Kalachikov, S|Gomez, S M|Krauthammer, M|Kaplan, S H|Kra, P|Russo, J J|Friedman, C', 'Columbia Genome Center, Columbia University, USA. ar345@columbia.edu|Columbia Genome Center, Columbia University, USA. ar345@columbia.edu|Columbia Genome Center, Columbia University, USA. ar345@columbia.edu|Columbia Genome Center, Columbia University, USA. ar345@columbia.edu|Columbia Genome Center, Columbia University, USA. ar345@columbia.edu|Columbia Genome Center, Columbia University, USA. ar345@columbia.edu|Columbia Genome Center, Columbia University, USA. ar345@columbia.edu|Columbia Genome Center, Columbia University, USA. ar345@columbia.edu|Columbia Genome Center, Columbia University, USA. ar345@columbia.edu', 'United States|United States|United States|United States|United States|United States|United States|United States|United States', 59, 'Animals|Artificial Intelligence|Classification|Computational Biology|Computer Simulation|Humans|Models, Biological|Natural Language Processing|Signal Transduction|Software', 'Comparative Study', '10.1093/bioinformatics/16.12.1120', '11159331', 'In order to aid in hypothesis-driven experimental gene discovery, we are designing a computer application for the automatic retrieval of signal transduction data from electronic versions of scientific publications using natural language processing (NLP) techniques, as well as for visualizing and editing representations of regulatory systems. These systems describe both signal transduction and biochemical pathways within complex multicellular organisms, yeast, and bacteria. This computer application in turn requires the development of a domain-specific ontology, or knowledge model.'),
(69862, 2000, 'bio', 'Semiotes: a semantics for sharing', 'Kazic, T', 'Institute for Biomedical Computing, Washington University, 700 South Euclid Avenue, St. Louis, MO 63110, USA. toni@athe.wustl.edu', 'United States', 10, 'Algorithms|Computational Biology|Databases, Factual|Semantics|Software', 'Journal Article', '10.1093/bioinformatics/16.12.1129', '11159332', 'Reliable, automated communication of biological information requires methods to declare the informations semantics. In this paper I describe an approach to semantic declaration intended to permit independent, distributed databases, algorithms, and servers to exchange and process requests for information and computations without requiring coordination or agreement among them on universe of discourse, data model, schema, or implementation.'),
(69863, 2000, 'bio', 'InterPro--an integrated documentation resource for protein families, domains and functional sites', 'Apweiler, R|Attwood, T K|Bairoch, A|Bateman, A|Birney, E|Biswas, M|Bucher, P|Cerutti, L|Corpet, F|Croning, M D|Durbin, R|Falquet, L|Fleischmann, W|Gouzy, J|Hermjakob, H|Hulo, N|Jonassen, I|Kahn, D|Kanapin, A|Karavidopoulou, Y|Lopez, R|Marx, B|Mulder, N J|Oinn, T M|Pagni, M|Servant, F|Sigrist, C J|Zdobnov, E M|InterPro Consortium', 'EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.|EMBL Outstation--European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK.', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|United Kingdom|', 201, 'Computational Biology|Computer Graphics|Databases, Factual|Internet|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/16.12.1145', '11159333', 'InterPro is a new integrated documentation resource for protein families, domains and functional sites, developed initially as a means of rationalising the complementary efforts of the PROSITE, PRINTS, Pfam and ProDom database projects.'),
(69864, 2000, 'bio', 'IE-Kb: intron exon knowledge base', 'Sakharkar, M K|Kangueane, P|Woon, T W|Tan, T W|Kolatkar, P R|Long, M|de Souza, S J', 'BioInformatics Centre, National University of Singapore, Singapore 119260, Singapore. meena@bic.nus.edu.sg|BioInformatics Centre, National University of Singapore, Singapore 119260, Singapore. meena@bic.nus.edu.sg|BioInformatics Centre, National University of Singapore, Singapore 119260, Singapore. meena@bic.nus.edu.sg|BioInformatics Centre, National University of Singapore, Singapore 119260, Singapore. meena@bic.nus.edu.sg|BioInformatics Centre, National University of Singapore, Singapore 119260, Singapore. meena@bic.nus.edu.sg|BioInformatics Centre, National University of Singapore, Singapore 119260, Singapore. meena@bic.nus.edu.sg|BioInformatics Centre, National University of Singapore, Singapore 119260, Singapore. meena@bic.nus.edu.sg', 'Singapore|Singapore|Singapore|Singapore|Singapore|Singapore|Singapore', 0, 'Artificial Intelligence|Computational Biology|Databases, Factual|Exons|Internet|Introns', 'Journal Article', '10.1093/bioinformatics/16.12.1151', '11159334', 'IE-Kb (Intron Exon-Knowledge base) illustrates the intron-exon dynamics in eukaryotic genes. We have developed three different knowledge sets, namely Non-redundant ExInt, Non-redundant Pfam-ExInt complement and Non-redundant GenBank eukaryotic subdivisional sets to understand this phenomenon. Statistical analysis is performed on each knowledge set and the results are made available online. The entries in knowledge sets are ranked based on their intron length, exon length and protein length with relational hyper-links to the corresponding intron phase, intron position, intron sequence, gene definition and parent GenBank entry.'),
(69865, 2000, 'bio', 'ASAP: analysis of peptide composition', 'Serra-Hartmann, X|Rebordosa, X|Piñol, J|Querol, E|Martí-Renom, M A', 'Institut de Biologia Fonamental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.|Institut de Biologia Fonamental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.|Institut de Biologia Fonamental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.|Institut de Biologia Fonamental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.|Institut de Biologia Fonamental, Universitat Autònoma de Barcelona, 08193 Bellaterra (Barcelona), Spain.', 'Spain|Spain|Spain|Spain|Spain', 0, 'Computational Biology|Databases, Factual|Internet|Oligopeptides|Proteins|Sequence Alignment|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/16.12.1153', '11159335', 'ASAP is a web tool designed to search for specific dipeptides, tripeptides and tetrapeptides in a protein sequence database. The server allows for: (a) identification of frequent and infrequent peptides and the creation of peptide probability tables for a given database of sequences (GenerNet program), (b) determination of the compatibility of an amino-acid sequence to the given peptide probability tables (ClonErrNet program), and (c) comparison of different protein databases based on peptide composition (CompNet program). ASAP server can be useful in protein engineering and/or protein classification studies.'),
(69866, 2000, 'bio', 'A simple probabilistic scoring method for protein domain identification', 'Murvai, J|Vlahovicek, K|Pongor, S', 'Protein Structure and Function Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy. murvai@icgeb.trieste.it|Protein Structure and Function Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy. murvai@icgeb.trieste.it|Protein Structure and Function Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy. murvai@icgeb.trieste.it', 'Italy|Italy|Italy', 12, 'Computational Biology|Databases, Factual|Internet|Models, Statistical|Protein Structure, Tertiary|Proteins|Sequence Alignment|Software', 'Comparative Study', '10.1093/bioinformatics/16.12.1155', '11159336', 'A simple heuristic scoring method is described for assigning sequences to known domain types based on BLAST search outputs. The scoring is based on the score distribution of the known domain groups determined from a database versus database comparison and is directly applicable to BLAST output processing.'),
(69867, 2000, 'bio', 'PANAL: an integrated resource for Protein sequence ANALysis', 'Silverstein, K A|Kilian, A|Freeman, J L|Johnson, J E|Awad, I A|Retzel, E F', 'Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE Minneapolis, MN 55455-0312, USA. panel@ahc.umn.edu|Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE Minneapolis, MN 55455-0312, USA. panel@ahc.umn.edu|Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE Minneapolis, MN 55455-0312, USA. panel@ahc.umn.edu|Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE Minneapolis, MN 55455-0312, USA. panel@ahc.umn.edu|Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE Minneapolis, MN 55455-0312, USA. panel@ahc.umn.edu|Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE Minneapolis, MN 55455-0312, USA. panel@ahc.umn.edu', 'United States|United States|United States|United States|United States|United States', 0, 'Computational Biology|Computer Graphics|Humans|Proteins|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/16.12.1157', '11159337', 'We present PANAL, an integrated resource for protein sequence analysis. The tool allows the user to simultaneously search a protein sequence for motifs from several databases, and to view the result as an intuitive graphical summary.'),
(69868, 2000, 'bio', 'A collection of well characterised integral membrane proteins', 'Möller, S|Kriventseva, E V|Apweiler, R', 'European Bioinformatics Institute, Cambridge, UK. moeller@ebi.ac.uk|European Bioinformatics Institute, Cambridge, UK. moeller@ebi.ac.uk|European Bioinformatics Institute, Cambridge, UK. moeller@ebi.ac.uk', 'United Kingdom|United Kingdom|United Kingdom', 89, 'Algorithms|Computational Biology|Internet|Membrane Proteins|Software', 'Journal Article', '10.1093/bioinformatics/16.12.1159', '11159338', 'A collection of transmembrane proteins with annotated transmembrane regions, for which good experimental evidence exist, was created as a test or training set for algorithms to predict transmembrane regions in proteins.'),
(69869, 2000, 'bio', 'TRITON: in silico construction of protein mutants and prediction of their activities', 'Prokop, M|Damborský, J|Koca, J', 'Laboratory of Biomolecular Structure and Dynamics, Masaryk University, Brno, Czech Republic. triton@chemi.muni.cz|Laboratory of Biomolecular Structure and Dynamics, Masaryk University, Brno, Czech Republic. triton@chemi.muni.cz|Laboratory of Biomolecular Structure and Dynamics, Masaryk University, Brno, Czech Republic. triton@chemi.muni.cz', '-|-|-', 0, 'Binding Sites|Catalysis|Computational Biology|Computer Simulation|Enzymes|Models, Chemical|Mutation|Protein Engineering|Sequence Homology, Amino Acid|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/16.9.845', '11187152', 'One of the objectives of protein engineering is to propose and construct modified proteins with improved activity for the substrate of interest. Systematic computational investigation of many protein variants requires the preparation and handling of a large number of data files. The type of the data generated during the modelling of protein variants and the estimation of their activities offers the possibility of process automatization.'),
(69870, 2001, 'bio', 'Registration of the expression patterns of Drosophila segmentation genes by two independent methods', 'Myasnikova, E|Samsonova, A|Kozlov, K|Samsonova, M|Reinitz, J', 'Institute of High Performance Computing and Data Bases, 118 Fontanka emb., St Petersburg 198005, Russia. myasnikova@fn.csa.ru|Institute of High Performance Computing and Data Bases, 118 Fontanka emb., St Petersburg 198005, Russia. myasnikova@fn.csa.ru|Institute of High Performance Computing and Data Bases, 118 Fontanka emb., St Petersburg 198005, Russia. myasnikova@fn.csa.ru|Institute of High Performance Computing and Data Bases, 118 Fontanka emb., St Petersburg 198005, Russia. myasnikova@fn.csa.ru|Institute of High Performance Computing and Data Bases, 118 Fontanka emb., St Petersburg 198005, Russia. myasnikova@fn.csa.ru', '-|-|-|-|-', 0, 'Algorithms|Animals|Chromosome Mapping|Computational Biology|Databases, Factual|Drosophila|Gene Expression Profiling|Gene Expression Regulation, Developmental|Genes, Insect|Software', 'Journal Article', '10.1093/bioinformatics/17.1.3', '11222257', 'To construct an integrated map of Drosophila segmentation gene expression from partial data taken from individual embryos.'),
(69871, 2001, 'bio', 'Pro-Frame: similarity-based gene recognition in eukaryotic DNA sequences with errors', 'Mironov, A A|Novichkov, P S|Gelfand, M S', 'State Scientific Center for Biotechnology NIIGenetika, Moscow, 113545, Russia.|State Scientific Center for Biotechnology NIIGenetika, Moscow, 113545, Russia.|State Scientific Center for Biotechnology NIIGenetika, Moscow, 113545, Russia.', '-|-|-', 22, 'Algorithms|Computational Biology|Frameshifting, Ribosomal|Humans|Proteins|Sequence Alignment|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/17.1.13', '11222258', 'Performance of existing algorithms for similarity-based gene recognition in eukaryotes drops when the genomic DNA has been sequenced with errors. A modification of the spliced alignment algorithm allows for gene recognition in sequences with errors, in particular frameshifts. It tolerates up to 5% of sequencing errors without considerable drop of prediction reliability when a sufficiently close homologous protein is available (normalized evolutionary distance similarity score 50% or higher).'),
(69872, 2001, 'bio', 'PAQ: Partition Analysis of Quasispecies', 'Baccam, P|Thompson, R J|Fedrigo, O|Carpenter, S|Cornette, J L', 'Department of Mathematics, Iowa State University, Ames, IA 50011, USA. pbaccam@lanl.gov|Department of Mathematics, Iowa State University, Ames, IA 50011, USA. pbaccam@lanl.gov|Department of Mathematics, Iowa State University, Ames, IA 50011, USA. pbaccam@lanl.gov|Department of Mathematics, Iowa State University, Ames, IA 50011, USA. pbaccam@lanl.gov|Department of Mathematics, Iowa State University, Ames, IA 50011, USA. pbaccam@lanl.gov', 'United States|United States|United States|United States|United States', 0, 'Algorithms|Animals|Cluster Analysis|Computational Biology|Databases, Factual|Evolution, Molecular|Genes, Viral|Genetic Techniques|HIV-1|Horses|Humans|Infectious Anemia Virus, Equine|Phylogeny|Software|Species Specificity', 'Journal Article', '10.1093/bioinformatics/17.1.16', '11222259', 'The complexities of genetic data may not be accurately described by any single analytical tool. Phylogenetic analysis is often used to study the genetic relationship among different sequences. Evolutionary models and assumptions are invoked to reconstruct trees that describe the phylogenetic relationship among sequences. Genetic databases are rapidly accumulating large amounts of sequences. Newly acquired sequences, which have not yet been characterized, may require preliminary genetic exploration in order to build models describing the evolutionary relationship among sequences. There are clustering techniques that rely less on models of evolution, and thus may provide nice exploratory tools for identifying genetic similarities. Some of the more commonly used clustering methods perform better when data can be grouped into mutually exclusive groups. Genetic data from viral quasispecies, which consist of closely related variants that differ by small changes, however, may best be partitioned by overlapping groups.'),
(69873, 2001, 'bio', 'Variations on probabilistic suffix trees: statistical modeling and prediction of protein families', 'Bejerano, G|Yona, G', 'School of Computer Science and Engineering, Hebrew University, Jerusalem 91904, Israel. jill@cs.huji.ac.il|School of Computer Science and Engineering, Hebrew University, Jerusalem 91904, Israel. jill@cs.huji.ac.il', 'Israel|Israel', 128, 'Algorithms|Computational Biology|Databases, Factual|Markov Chains|Models, Statistical|Proteins|Sequence Alignment|Sequence Analysis, Protein|Software', 'Comparative Study', '10.1093/bioinformatics/17.1.23', '11222260', 'We present a method for modeling protein families by means of probabilistic suffix trees (PSTs). The method is based on identifying significant patterns in a set of related protein sequences. The patterns can be of arbitrary length, and the input sequences do not need to be aligned, nor is delineation of domain boundaries required. The method is automatic, and can be applied, without assuming any preliminary biological information, with surprising success. Basic biological considerations such as amino acid background probabilities, and amino acids substitution probabilities can be incorporated to improve performance.');
INSERT INTO `papers` (`id`, `ano`, `journal`, `titulo`, `autores`, `afiliacao`, `pais`, `citacoes`, `palavra_chave`, `categorias`, `doi`, `pubmed`, `abstract`) VALUES
(69874, 2001, 'bio', 'Functional and structural genomics using PEDANT', 'Frishman, D|Albermann, K|Hani, J|Heumann, K|Metanomski, A|Zollner, A|Mewes, H W', 'GSF-Forschungszentrum für Umwelt und Gesundheit, Munich Information Center for Protein Sequences, Martinsried, Germany. frishman@mips.biochem.mpg.de|GSF-Forschungszentrum für Umwelt und Gesundheit, Munich Information Center for Protein Sequences, Martinsried, Germany. frishman@mips.biochem.mpg.de|GSF-Forschungszentrum für Umwelt und Gesundheit, Munich Information Center for Protein Sequences, Martinsried, Germany. frishman@mips.biochem.mpg.de|GSF-Forschungszentrum für Umwelt und Gesundheit, Munich Information Center for Protein Sequences, Martinsried, Germany. frishman@mips.biochem.mpg.de|GSF-Forschungszentrum für Umwelt und Gesundheit, Munich Information Center for Protein Sequences, Martinsried, Germany. frishman@mips.biochem.mpg.de|GSF-Forschungszentrum für Umwelt und Gesundheit, Munich Information Center for Protein Sequences, Martinsried, Germany. frishman@mips.biochem.mpg.de|GSF-Forschungszentrum für Umwelt und Gesundheit, Munich Information Center for Protein Sequences, Martinsried, Germany. frishman@mips.biochem.mpg.de', 'Germany|Germany|Germany|Germany|Germany|Germany|Germany', 0, 'Arabidopsis|Chaperonin 60|Computational Biology|Databases, Factual|Expressed Sequence Tags|Genome, Fungal|Genomics|Humans|Internet|Proteins|Saccharomyces cerevisiae|Sequence Analysis, DNA|Sequence Analysis, Protein|Software', 'Comparative Study', '10.1093/bioinformatics/17.1.44', '11222261', 'Enormous demand for fast and accurate analysis of biological sequences is fuelled by the pace of genome analysis efforts. There is also an acute need in reliable up-to-date genomic databases integrating both functional and structural information. Here we describe the current status of the PEDANT software system for high-throughput analysis of large biological sequence sets and the genome analysis server associated with it.'),
(69875, 2001, 'bio', 'Alignment of 3D structures of macromolecular assemblies', 'Lanzavecchia, S|Cantele, F|Bellon, P L', 'Universitàdi Milano, Dipartimento di Chimica Strutturale e Stereochimica Inorganica Via G. Venezian 21, 20133 Milano, Italy. salvator@csmtbo.mi.cnr.it|Universitàdi Milano, Dipartimento di Chimica Strutturale e Stereochimica Inorganica Via G. Venezian 21, 20133 Milano, Italy. salvator@csmtbo.mi.cnr.it|Universitàdi Milano, Dipartimento di Chimica Strutturale e Stereochimica Inorganica Via G. Venezian 21, 20133 Milano, Italy. salvator@csmtbo.mi.cnr.it', 'Italy|Italy|Italy', 13, 'Algorithms|Computational Biology|Image Processing, Computer-Assisted|Macromolecular Substances|Microscopy, Electron|Models, Molecular|Software', 'Journal Article', '10.1093/bioinformatics/17.1.58', '11222262', 'A number of macromolecular assemblies are being reconstructed in 3D from electron micrographs. The analysis yields a 3D matrix representing the protein density map. In reconstruction processes and in comparing the results of different experiments, it is often necessary to obtain all models oriented the same way in three dimensions. The problem is not trivial since there exist no 3D counterpart of correlation analysis used for 2D images. It is usually solved by time consuming trial and error algorithms.'),
(69876, 2001, 'bio', 'What are the baselines for protein fold recognition?', 'McGuffin, L J|Bryson, K|Jones, D T', 'Bioinformatics Group, Department of Biological Sciences, Brunel University, Uxbridge UB8 3PH, UK.|Bioinformatics Group, Department of Biological Sciences, Brunel University, Uxbridge UB8 3PH, UK.|Bioinformatics Group, Department of Biological Sciences, Brunel University, Uxbridge UB8 3PH, UK.', 'United Kingdom|United Kingdom|United Kingdom', 6, 'Computational Biology|Databases, Factual|Protein Folding|Protein Structure, Secondary|Protein Structure, Tertiary|Reproducibility of Results|Sensitivity and Specificity', 'Comparative Study', '10.1093/bioinformatics/17.1.63', '11222263', 'What constitutes a baseline level of success for protein fold recognition methods? As fold recognition benchmarks are often presented without any thought to the results that might be expected from a purely random set of predictions, an analysis of fold recognition baselines is long overdue. Given varying amounts of basic information about a protein-ranging from the length of the sequence to a knowledge of its secondary structure-to what extent can the fold be determined by intelligent guesswork? Can simple methods that make use of secondary structure information assign folds more accurately than purely random methods and could these methods be used to construct viable hierarchical classifications? EXPERIMENTS PERFORMED: A number of rapid automatic methods which score similarities between protein domains were devised and tested. These methods ranged from those that incorporated no secondary structure information, such as measuring absolute differences in sequence lengths, to more complex alignments of secondary structure elements. Each method was assessed for accuracy by comparison with the Class Architecture Topology Homology (CATH) classification. Methods were rated against both a random baseline fold assignment method as a lower control and FSSP as an upper control. Similarity trees were constructed in order to evaluate the accuracy of optimum methods at producing a classification of structure.'),
(69877, 2001, 'bio', 'A Web interface generator for molecular biology programs in Unix', 'Letondal, C', 'Institut Pasteur, Service dInformatique Scientifique, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France. pise@pasteur.fr', 'France', 0, 'Computational Biology|Internet|Molecular Biology|Programming Languages|Sequence Analysis|Software|User-Computer Interface', 'Journal Article', '10.1093/bioinformatics/17.1.73', '11222264', 'Almost all users encounter problems using sequence analysis programs. Not only are they difficult to learn because of the parameters, syntax and semantic, but many are different. That is why we have developed a Web interface generator for more than 150 molecular biology command-line driven programs, including: phylogeny, gene prediction, alignment, RNA, DNA and protein analysis, motif discovery, structure analysis and database searching programs. The generator uses XML as a high-level description language of the legacy software parameters. Its aim is to provide users with the equivalent of a basic Unix environment, with program combination, customization and basic scripting through macro registration.'),
(69878, 2001, 'bio', 'ISYS: a decentralized, component-based approach to the integration of heterogeneous bioinformatics resources', 'Siepel, A|Farmer, A|Tolopko, A|Zhuang, M|Mendes, P|Beavis, W|Sobral, B', 'National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA. isys@ncgr.org|National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA. isys@ncgr.org|National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA. isys@ncgr.org|National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA. isys@ncgr.org|National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA. isys@ncgr.org|National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA. isys@ncgr.org|National Center for Genome Resources, 2935 Rodeo Park Drive East, Santa Fe, NM 87505, USA. isys@ncgr.org', 'United States|United States|United States|United States|United States|United States|United States', 51, 'Arabidopsis|Computational Biology|Databases, Factual|Genome, Plant|Quantitative Trait, Heritable|Software', 'Journal Article', '10.1093/bioinformatics/17.1.83', '11222265', 'Heterogeneity of databases and software resources continues to hamper the integration of biological information. Top-down solutions are not feasible for the full-scale problem of integration across biological species and data types. Bottom-up solutions so far have not integrated, in a maximally flexible way, dynamic and interactive graphical-user-interface components with data repositories and analysis tools.'),
(69879, 2001, 'bio', 'Transcription-associated protein families are primarily taxon-specific', 'Coulson, R M|Enright, A J|Ouzounis, C A', 'Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.|Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.|Computational Genomics Group, Research Programme, The European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge CB10 1SD, UK.', 'United Kingdom|United Kingdom|United Kingdom', 0, 'Computational Biology|Databases, Factual|Phylogeny|Proteins|Transcription Factors|Transcription, Genetic', 'Journal Article', '10.1093/bioinformatics/17.1.95', '11222266', 'The mechanisms controlling gene regulation appear to be fundamentally different in eukaryotes and prokaryotes (Struhl (1999) CELL, 98, 1-4). To investigate this diversity further, we have analysed the distribution of all known transcription-associated proteins (TAPs), as reflected by sequence database annotations. Our results for the primary phylogenetic domains (Archaea, Bacteria and Eukaryota) show that TAP families are mostly taxon-specific and very few transcriptional regulators are common across these domains.'),
(69880, 2001, 'bio', 'PrimeArray: genome-scale primer design for DNA-microarray construction', 'Raddatz, G|Dehio, M|Meyer, T F|Dehio, C', 'Max-Planck-Institut für Biologie, Abteilung Infektionsbiologie, Spemannstrasse 34, 72076 Tübingen, Germany.|Max-Planck-Institut für Biologie, Abteilung Infektionsbiologie, Spemannstrasse 34, 72076 Tübingen, Germany.|Max-Planck-Institut für Biologie, Abteilung Infektionsbiologie, Spemannstrasse 34, 72076 Tübingen, Germany.|Max-Planck-Institut für Biologie, Abteilung Infektionsbiologie, Spemannstrasse 34, 72076 Tübingen, Germany.', 'Germany|Germany|Germany|Germany', 48, 'Base Sequence|Computational Biology|Computer-Aided Design|DNA Primers|Drug Design|Helicobacter pylori|Oligonucleotide Array Sequence Analysis|Polymerase Chain Reaction|Software', 'Journal Article', '10.1093/bioinformatics/17.1.98', '11222267', 'PrimeArray is a Windows program that computes oligonuceotide primer pairs for genome-scale gene amplification by the Polymerase Chain Reaction (PCR). The program supports the automated extraction of coding sequences (CDS) from various input-file formats and allows highly automated primer pair-optimization.'),
(69881, 2001, 'bio', 'The PACRAT system: an extensible WWW-based system for correlated sequence retrieval, storage and analysis', 'Ray, W C|Daniels, C J', 'Biophysics Program and Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA. ray@biosci.ohio-state.edu|Biophysics Program and Department of Microbiology, The Ohio State University, Columbus, OH 43210, USA. ray@biosci.ohio-state.edu', 'United States|United States', 3, 'Computational Biology|Databases, Factual|Genomics|Internet|Sequence Analysis|Software', 'Journal Article', '10.1093/bioinformatics/17.1.100', '11222268', 'With PACRAT (Patterns, Analyses, Correlations. Remote Archive Testbed) we present an online database solution to the problem of accessing high-confidence sequences with specific relationships to classes of genes, such as upstream intergenic regions attached to tRNA genes. In addition the software contains a data warehousing and analysis-facilitating suite to streamline the process of analyzing the collected data. An unexpected additional benefit of the system is that it also provides easy access to sequences of lower confidence, and may be of assistance in such things as resolving ORF-call conflicts in genomic annotation projects.'),
(69882, 2001, 'bio', 'EASY--an Expert Analysis SYstem for interpreting database search outputs', 'Selley, J N|Swift, J|Attwood, T K', 'School of Biological Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK. selley@bioinf.man.ac.uk|School of Biological Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK. selley@bioinf.man.ac.uk|School of Biological Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK. selley@bioinf.man.ac.uk', 'United Kingdom|United Kingdom|United Kingdom', 6, 'Computational Biology|Databases, Factual|Expert Systems|Proteins|Sequence Analysis, Protein|Software', 'Journal Article', '10.1093/bioinformatics/17.1.105', '11222269', 'With the ever-increasing need to handle large volumes of sequence data efficiently and reliably, we have developed the EASY system for performing combined protein sequence and pattern database searches. EASY runs searches simultaneously and distils results into a concise 1-line diagnosis. By bringing together results of several different analyses, EASY provides a rapid means of evaluating biological significance, minimising the risk of inferring false relationships, for example from relying exclusively on top BLAST hits. The program has been tested using a variety of protein families and was instrumental in resolving family assignments in a major update of the PRINTS database.'),
(69883, 2001, 'bio', 'On the importance of standardisation in life sciences', 'Brazma, A', 'School of Biological Sciences, The University of Manchester, Oxford Road, Manchester, M13 9PT, UK. selley@bioinf.man.ac.uk', 'United Kingdom', 21, 'Biological Science Disciplines|Databases, Factual|Gene Expression Profiling|Humans|Information Storage and Retrieval|Oligonucleotide Array Sequence Analysis|Sequence Analysis, DNA', 'Editorial', '10.1093/bioinformatics/17.2.113', '11238066', '-'),
(69884, 2001, 'bio', 'XML, bioinformatics and data integration', 'Achard, F|Vaysseix, G|Barillot, E', 'CRI Infobiogen, 523 place des terrasses de lagora, 91000 Evry, France.|CRI Infobiogen, 523 place des terrasses de lagora, 91000 Evry, France.|CRI Infobiogen, 523 place des terrasses de lagora, 91000 Evry, France.', 'France|France|France', 27, 'Computational Biology|Humans|Information Storage and Retrieval|Internet|Programming Languages', 'Journal Article', '10.1093/bioinformatics/17.2.115', '11238067', 'The eXtensible Markup Language (XML) is an emerging standard for structuring documents, notably for the World Wide Web. In this paper, the authors present XML and examine its use as a data language for bioinformatics. In particular, XML is compared to other languages, and some of the potential uses of XML in bioinformatics applications are presented. The authors propose to adopt XML for data interchange between databases and other sources of data. Finally the discussion is illustrated by a test case of a pedigree data model in XML.'),
(69885, 2001, 'bio', 'A hierarchical unsupervised growing neural network for clustering gene expression patterns', 'Herrero, J|Valencia, A|Dopazo, J', 'Bioinformatics, CNIO, Ctra. Majadahonda-Pozuelo, Km 2, Majadahonda, 28220 Madrid Protein Design Group CNB-CSIC, 28049 Madrid, Spain.|Bioinformatics, CNIO, Ctra. Majadahonda-Pozuelo, Km 2, Majadahonda, 28220 Madrid Protein Design Group CNB-CSIC, 28049 Madrid, Spain.|Bioinformatics, CNIO, Ctra. Majadahonda-Pozuelo, Km 2, Majadahonda, 28220 Madrid Protein Design Group CNB-CSIC, 28049 Madrid, Spain.', 'Spain|Spain|Spain', 0, 'Algorithms|Electronic Data Processing|Gene Expression Profiling|Neural Networks (Computer)|Oligonucleotide Array Sequence Analysis', 'Journal Article', '10.1093/bioinformatics/17.2.126', '11238068', 'We describe a new approach to the analysis of gene expression data coming from DNA array experiments, using an unsupervised neural network. DNA array technologies allow monitoring thousands of genes rapidly and efficiently. One of the interests of these studies is the search for correlated gene expression patterns, and this is usually achieved by clustering them. The Self-Organising Tree Algorithm, (SOTA) (Dopazo,J. and Carazo,J.M. (1997) J. Mol. Evol., 44, 226-233), is a neural network that grows adopting the topology of a binary tree. The result of the algorithm is a hierarchical cluster obtained with the accuracy and robustness of a neural network.'),
(69886, 2001, 'bio', 'The massively parallel genetic algorithm for RNA folding: MIMD implementation and population variation', 'Shapiro, B A|Wu, J C|Bengali, D|Potts, M J', 'Image Processing Section, Laboratory of Experimental and Computational Biology, Division of Basic Sciences, National Cancer Institute, Frederick Cancer Research and Development Center, National Institutes of Health, Bldg 469, Frederick, MD 21702, USA.|Image Processing Section, Laboratory of Experimental and Computational Biology, Division of Basic Sciences, National Cancer Institute, Frederick Cancer Research and Development Center, National Institutes of Health, Bldg 469, Frederick, MD 21702, USA.|Image Processing Section, Laboratory of Experimental and Computational Biology, Division of Basic Sciences, National Cancer Institute, Frederick Cancer Research and Development Center, National Institutes of Health, Bldg 469, Frederick, MD 21702, USA.|Image Processing Section, Laboratory of Experimental and Computational Biology, Division of Basic Sciences, National Cancer Institute, Frederick Cancer Research and Development Center, National Institutes of Health, Bldg 469, Frederick, MD 21702, USA.', 'United States|United States|United States|United States', 74, 'Algorithms|Computers|Databases, Factual|Nucleic Acid Conformation|RNA|Sequence Analysis, RNA', 'Journal Article', '10.1093/bioinformatics/17.2.137', '11238069', 'A massively parallel Genetic Algorithm (GA) has been applied to RNA sequence folding on three different computer architectures. The GA, an evolution-like algorithm that is applied to a large population of RNA structures based on a pool of helical stems derived from an RNA sequence, evolves this population in parallel. The algorithm was originally designed and developed for a 16384 processor SIMD (Single Instruction Multiple Data) MasPar MP-2. More recently it has been adapted to a 64 processor MIMD (Multiple Instruction Multiple Data) SGI ORIGIN 2000, and a 512 processor MIMD CRAY T3E. The MIMD version of the algorithm raises issues concerning RNA structure data-layout and processor communication. In addition, the effects of population variation on the predicted results are discussed. Also presented are the scaling properties of the algorithm from the perspective of the number of physical processors utilized and the number of virtual processors (RNA structures) operated upon.'),
(69887, 2001, 'bio', 'An information-based sequence distance and its application to whole mitochondrial genome phylogeny', 'Li, M|Badger, J H|Chen, X|Kwong, S|Kearney, P|Zhang, H', 'Bioinformatics Laboratory, Computer Science Department, University of Waterloo, N2L 3G1, Canada. mli@wh.math.uwaterloo.ca|Bioinformatics Laboratory, Computer Science Department, University of Waterloo, N2L 3G1, Canada. mli@wh.math.uwaterloo.ca|Bioinformatics Laboratory, Computer Science Department, University of Waterloo, N2L 3G1, Canada. mli@wh.math.uwaterloo.ca|Bioinformatics Laboratory, Computer Science Department, University of Waterloo, N2L 3G1, Canada. mli@wh.math.uwaterloo.ca|Bioinformatics Laboratory, Computer Science Department, University of Waterloo, N2L 3G1, Canada. mli@wh.math.uwaterloo.ca|Bioinformatics Laboratory, Computer Science Department, University of Waterloo, N2L 3G1, Canada. mli@wh.math.uwaterloo.ca', 'Canada|Canada|Canada|Canada|Canada|Canada', 44, 'Animals|DNA, Mitochondrial|Humans|Mathematical Computing|Phylogeny|Rodentia|Sequence Alignment|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/17.2.149', '11238070', 'Traditional sequence distances require an alignment and therefore are not directly applicable to the problem of whole genome phylogeny where events such as rearrangements make full length alignments impossible. We present a sequence distance that works on unaligned sequences using the information theoretical concept of Kolmogorov complexity and a program to estimate this distance.'),
(69888, 2001, 'bio', 'Automated extraction of information on protein-protein interactions from the biological literature', 'Ono, T|Hishigaki, H|Tanigami, A|Takagi, T', 'Otsuka GEN Research Institute, Otsuka Pharmaceutical Co. Ltd, 463-10 Kagasuno, Kawauchi-cho, Tokushima, 771-0192, Japan. ono@otsuka.gr.jp|Otsuka GEN Research Institute, Otsuka Pharmaceutical Co. Ltd, 463-10 Kagasuno, Kawauchi-cho, Tokushima, 771-0192, Japan. ono@otsuka.gr.jp|Otsuka GEN Research Institute, Otsuka Pharmaceutical Co. Ltd, 463-10 Kagasuno, Kawauchi-cho, Tokushima, 771-0192, Japan. ono@otsuka.gr.jp|Otsuka GEN Research Institute, Otsuka Pharmaceutical Co. Ltd, 463-10 Kagasuno, Kawauchi-cho, Tokushima, 771-0192, Japan. ono@otsuka.gr.jp', 'Japan|Japan|Japan|Japan', 63, 'Electronic Data Processing|Information Storage and Retrieval|Literature|Proteins', 'Journal Article', '10.1093/bioinformatics/17.2.155', '11238071', 'To understand biological process, we must clarify how proteins interact with each other. However, since information about protein-protein interactions still exists primarily in the scientific literature, it is not accessible in a computer-readable format. Efficient processing of large amounts of interactions therefore needs an intelligent information extraction method. Our aim is to develop an efficient method for extracting information on protein-protein interaction from scientific literature.'),
(69889, 2001, 'bio', 'GeneOrder: comparing the order of genes in small genomes', 'Mazumder, R|Kolaskar, A|Seto, D', 'School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 4E3, Manassas, VA 20110, USA.|School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 4E3, Manassas, VA 20110, USA.|School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 4E3, Manassas, VA 20110, USA.', 'United States|United States|United States', 0, 'Animals|Databases, Factual|Humans|Internet|Proteins|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/17.2.162', '11238072', 'The recent rapid rise in the availability of whole genome DNA sequence data has led to bottlenecks in their complete analysis. Specifically, there is a need for software tools that will allow mining of gene and putative gene data at a whole genome level. These new tools will complement the current set already in use for studying specific aspects of individual genes and putative genes in detail. A key software challenge is to make them user-friendly, without losing their flexibility and capability for use in research.'),
(69890, 2001, 'bio', 'ORI-GENE: gene classification based on the evolutionary tree', 'Mizuno, H|Tanaka, Y|Nakai, K|Sarai, A', 'Institute of Biological Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan. hideaki.mizuno@roche.com|Institute of Biological Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan. hideaki.mizuno@roche.com|Institute of Biological Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan. hideaki.mizuno@roche.com|Institute of Biological Sciences, University of Tsukuba, 1-1-1 Ten-nodai, Tsukuba, Ibaraki 305-8572, Japan. hideaki.mizuno@roche.com', 'Japan|Japan|Japan|Japan', 1, 'Animals|Evolution, Molecular|Genes|Humans|Sequence Alignment|Sequence Homology, Nucleic Acid|Software', 'Journal Article', '10.1093/bioinformatics/17.2.167', '11238073', 'Genome projects have produced large amounts of data on the sequences of new genes whose functions are as yet unknown. The functions of new genes are usually inferred by comparing their sequences with those of known genes, but evaluation of the sequence homology of individual genes does not make the most of the available sequence information. Therefore, new methods and tools for extracting more biological information from homology searches would be advantageous.'),
(69891, 2001, 'bio', 'The art of pedigree drawing: algorithmic aspects', 'Tores, F|Barillot, E', 'GIS Infobiogen, 7 rue Guy Môquet, BP 8, 94801 Villejuif cedex Généthon, 1 bis rue de lInternationale, 91000 Evry, France.|GIS Infobiogen, 7 rue Guy Môquet, BP 8, 94801 Villejuif cedex Généthon, 1 bis rue de lInternationale, 91000 Evry, France.', 'France|France', 13, 'Algorithms|Computer Graphics|Pedigree', 'Journal Article', '10.1093/bioinformatics/17.2.174', '11238074', 'Giving a meaningful representation of a pedigree is not obvious when it includes consanguinity loops, individuals with multiple mates or several related families.'),
(69892, 2001, 'bio', 'A classification of tasks in bioinformatics', 'Stevens, R|Goble, C|Baker, P|Brass, A', 'Department of Computer Science School of Biological Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.|Department of Computer Science School of Biological Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.|Department of Computer Science School of Biological Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.|Department of Computer Science School of Biological Sciences, The University of Manchester, Oxford Road, Manchester M13 9PL, UK.', 'United Kingdom|United Kingdom|United Kingdom|United Kingdom', 0, 'Computational Biology|Research|Surveys and Questionnaires', 'Journal Article', '10.1093/bioinformatics/17.2.180', '11238075', 'This paper reports on a survey of bioinformatics tasks currently undertaken by working biologists. The aim was to find the range of tasks that need to be supported and the components needed to do this in a general query system. This enabled a set of evaluation criteria to be used to assess both the biology and mechanical nature of general query systems.'),
(69893, 2001, 'bio', 'Distribution of genes for lysine biosynthesis through the aminoadipate pathway among prokaryotic genomes', 'Nishida, H', 'Institute of Molecular and Cellular Biosciences, University of Tokyo, Tokyo 113-0032, Japan. hnishida@iam.u-tokyo.ac.jp', 'Japan', 12, 'Amino Acid Sequence|Lysine|Molecular Sequence Data|Multigene Family|Prokaryotic Cells|Thermus thermophilus', 'Journal Article', '10.1093/bioinformatics/17.2.189', '11238076', 'Deinococcus radioduranshas homologous genes to the genes which from the Thermus: thermophilus gene cluster for lysine biosynthesis. Interestingly, those genes are clustered in Thermus, nevertheless they are scattered in Deinococcus. A similar gene cluster has only been found in Pyrococcus However, the phylogenetic analyses indicated that the deduced gene products from Deinococcus were the most closely related to the proteins encoded in the Thermus gene cluster for lysine biosynthesis. Therefore, those genes had not been transferred horizontally between Pyrococcus and Thermus. It is strongly suggested that a common ancestor of Deinococcus and Thermus possessed the genes for lysine biosynthesis through the aminoadipate pathway. These had been clustered through the evolution of Thermus or had been scattered from the gene cluster through the evolution of Deinococcus. In addition, I showed that LysW and its homologues were specialized proteins for the prokaryotic lysine biosynthesis through the aminoadipate pathway.'),
(69894, 2001, 'bio', 'Virtual PCR', 'Lexa, M|Horak, J|Brzobohaty, B', 'Laboratory of Plant Molecular Physiology, Masaryk University Brno, Faculty of Science, Kotlarska 2, 611 37, Brno, Czech Republic. m-lexa@sci.muni.cz|Laboratory of Plant Molecular Physiology, Masaryk University Brno, Faculty of Science, Kotlarska 2, 611 37, Brno, Czech Republic. m-lexa@sci.muni.cz|Laboratory of Plant Molecular Physiology, Masaryk University Brno, Faculty of Science, Kotlarska 2, 611 37, Brno, Czech Republic. m-lexa@sci.muni.cz', '-|-|-', 0, 'Algorithms|DNA Primers|Databases, Factual|Polymerase Chain Reaction|Software', 'Journal Article', '10.1093/bioinformatics/17.2.192', '11238077', 'We present an algorithm that uses public sequence data to predict PCR products. The algorithm is implemented as a CGI script. Output is compared to real-world PCR.'),
(69895, 2001, 'bio', 'Using clusters of computers for large QU-GENE simulation experiments', 'Micallef, K P|Cooper, M|Podlich, D W', 'School of Land and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia. k.micallef@mailbox.uq.edu.au|School of Land and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia. k.micallef@mailbox.uq.edu.au|School of Land and Food Sciences, The University of Queensland, Brisbane, Queensland 4072, Australia. k.micallef@mailbox.uq.edu.au', 'Australia|Australia|Australia', 5, 'Computer Simulation|Computers|Genes|Models, Genetic|Software', 'Journal Article', '10.1093/bioinformatics/17.2.194', '11238078', 'The QU-GENE Computing Cluster (QCC) is a hardware and software solution to the automation and speedup of large QU-GENE (QUantitative GENEtics) simulation experiments that are designed to examine the properties of genetic models, particularly those that involve factorial combinations of treatment levels. QCC automates the management of the distribution of components of the simulation experiments among the networked single-processor computers to achieve the speedup.'),
(69896, 2001, 'bio', 'MOSAIC: segmenting multiple aligned DNA sequences', 'André, C|Vincens, P|Boisvieux, J F|Hazout, S', 'Département de Biomathématiques, UniversitéParis 6, CHU Pitié-Salpêtrière, 91 boulevard de lHôpital, 75634 Paris Cedex 13, France. can@biomath.jussieu.fr|Département de Biomathématiques, UniversitéParis 6, CHU Pitié-Salpêtrière, 91 boulevard de lHôpital, 75634 Paris Cedex 13, France. can@biomath.jussieu.fr|Département de Biomathématiques, UniversitéParis 6, CHU Pitié-Salpêtrière, 91 boulevard de lHôpital, 75634 Paris Cedex 13, France. can@biomath.jussieu.fr|Département de Biomathématiques, UniversitéParis 6, CHU Pitié-Salpêtrière, 91 boulevard de lHôpital, 75634 Paris Cedex 13, France. can@biomath.jussieu.fr', 'France|France|France|France', 0, 'Genome, Fungal|Saccharomyces cerevisiae|Sequence Alignment|Sequence Analysis, DNA|Software', 'Journal Article', '10.1093/bioinformatics/17.2.196', '11238079', 'MOSAIC is a set of tools for the segmentation of multiple aligned DNA sequences into homogeneous zones. The segmentation is based on the distribution of mutational events along the alignment. As an example, the analysis of one repeated sequence belonging to the subtelomeric regions of the yeast genome is presented.'),
(69897, 2001, 'bio', 'COMBOSA3D: combining sequence alignments with three-dimensional structures', 'Stothard, P M', 'Department of Biological Sciences, University of Alberta, Edmonton, Alberta, T6G 2E9, Canada. stothard@ualberta.ca', 'Canada', 7, 'Animals|Computer Simulation|Humans|Models, Molecular|Protein Conformation|Proteins|Sequence Alignment|Software', 'Journal Article', '10.1093/bioinformatics/17.2.198', '11238080', 'COMBOSA3D is a program that allows sequence conservation to be viewed in its proper three-dimensional environment. It superimposes sequence alignment information onto a protein structure using a customizable color scheme, which is also applied to a textual sequence alignment for reference.'),
(69898, 2001, 'bio', '3Dee: a database of protein structural domains', 'Siddiqui, A S|Dengler, U|Barton, G J', 'University of Oxford, Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK.|University of Oxford, Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK.|University of Oxford, Laboratory of Molecular Biophysics, The Rex Richards Building, South Parks Road, Oxford OX1 3QU, UK.', 'United Kingdom|United Kingdom|United Kingdom', 0, 'Databases, Factual|Protein Structure, Tertiary|Proteins', 'Journal Article', '10.1093/bioinformatics/17.2.200', '11238081', 'The 3Dee database is a repository of protein structural domains. It stores alternative domain definitions for the same protein, organises domains into sequence and structural hierarchies, contains non-redundant set(s) of sequences and structures, multiple structure alignments for families of domains, and allows previous versions of the database to be regenerated.'),
(69899, 2001, 'bio', 'RCNPRED: prediction of the residue co-ordination numbers in proteins', 'Fariselli, P|Casadio, R', 'CIRB Biocomputing Unit, Department of Biology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy. piero@lipid.biocomp.unibo.it|CIRB Biocomputing Unit, Department of Biology, University of Bologna, via Irnerio 42, 40126 Bologna, Italy. piero@lipid.biocomp.unibo.it', 'Italy|Italy', 14, 'Databases, Factual|Neural Networks (Computer)|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/17.2.202', '11238082', 'The RCNPRED server implements a neural network-based method to predict the co-ordination numbers of residues starting from the protein sequence. Using evolutionary information as input, RCNPRED predicts the residue states of the proteins in the database with 69% accuracy and scores 12 percentage points higher than a simple statistical method. Moreover the server implements a neural network to predict the relative solvent accessibility of each residue. A protein sequence can be directly submitted to RCNPRED: residue co-ordination numbers and solvent accessibility for each chain are returned via e-mail.'),
(69900, 2000, 'bio', 'Modelit: building three dimensional DNA models from sequence data', 'Vlahovicek, K|Pongor, S', 'Protein Structure and Function Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy. kristian@icgeb.trieste.it|Protein Structure and Function Group, International Centre for Genetic Engineering and Biotechnology, Area Science Park, 34012 Trieste, Italy. kristian@icgeb.trieste.it', 'Italy|Italy', 0, 'Base Sequence|Computational Biology|DNA|DNA, Plant|Databases, Factual|Internet|Models, Molecular|Nucleic Acid Conformation|Promoter Regions, Genetic|Sequence Alignment|Software|Zea mays', 'Journal Article', '10.1093/bioinformatics/16.11.1044', '11269231', 'A WWW server is described for creating 3D models of canonical or bent DNA starting from sequence data. Predicted DNA trajectory is first computed based on a choice of di- and tri-nucleotide models (M.G. Munteanu et al., Trends Biochem. Sci. 23, 341-347, 1998), an atomic model is then constructed and optionally energy-minimized with constrained molecular dynamics. The data are presented as a standard PDB file, directly viewable on the users PC using any molecule manipulation program.'),
(69901, 2001, 'bio', 'Physical mapping with automatic capture of hybridization data', 'Hall, D|Bhandarkar, S M|Arnold, J|Jiang, T', 'Department of Computer Science, The University of Georgia, Athens, GA 30602, USA.|Department of Computer Science, The University of Georgia, Athens, GA 30602, USA.|Department of Computer Science, The University of Georgia, Athens, GA 30602, USA.|Department of Computer Science, The University of Georgia, Athens, GA 30602, USA.', 'Georgia|Georgia|Georgia|Georgia', 7, 'Algorithms|Aspergillus nidulans|Automation|Contig Mapping|DNA, Fungal|Electronic Data Processing|Nucleic Acid Hybridization|Software', 'Journal Article', '10.1093/bioinformatics/17.3.205', '11294786', 'Contig maps are a type of physical map that show the native order of a set of overlapping genomic clones. Overlaps between clones can be detected by finding common sequences using a number of experimental protocols including hybridization of probes. All current mapping algorithms of which we are aware require that hybridizations be scored using a fixed number of discrete values (typically 0/1 or high/medium/low). When hybridization data is captured automatically using digital equipment, this provides the opportunity for hybridization intensities to be used in map construction. More fine-grained distinctions in the levels of hybridization may be exploited by algorithms to generate more accurate physical maps.'),
(69902, 2001, 'bio', 'Efficient primer design algorithms', 'Kämpke, T|Kieninger, M|Mecklenburg, M', 'Forschungsinstitut für anwendungsorientierte Wissensverarbeitung FAW, Helmholtzstr. 16, 89081 Ulm, Germany. kaempke@faw.uni-ulm.de|Forschungsinstitut für anwendungsorientierte Wissensverarbeitung FAW, Helmholtzstr. 16, 89081 Ulm, Germany. kaempke@faw.uni-ulm.de|Forschungsinstitut für anwendungsorientierte Wissensverarbeitung FAW, Helmholtzstr. 16, 89081 Ulm, Germany. kaempke@faw.uni-ulm.de', 'Germany|Germany|Germany', 65, 'Algorithms|DNA Primers|Polymerase Chain Reaction|Software', 'Journal Article', '10.1093/bioinformatics/17.3.214', '11294787', 'Primer design involves various parameters such as string-based alignment scores, melting temperature, primer length and GC content. This entails a design approach from multicriteria decision making. Values of some of the criteria are easy to compute while others require intense calculations.'),
(69903, 2001, 'bio', 'Basic Gene Grammars and DNA-ChartParser for language processing of Escherichia coli promoter DNA sequences', 'Leung , S|Mellish, C|Robertson, D', 'Division of Informatics, University of Edinburgh, 80 South Bridge, Edinburgh EH1 1HN, UK. siu@daied.ac.uk|Division of Informatics, University of Edinburgh, 80 South Bridge, Edinburgh EH1 1HN, UK. siu@daied.ac.uk|Division of Informatics, University of Edinburgh, 80 South Bridge, Edinburgh EH1 1HN, UK. siu@daied.ac.uk', 'United Kingdom|United Kingdom|United Kingdom', 28, 'DNA, Bacterial|Escherichia coli|Genes, Bacterial|Programming Languages|Promoter Regions, Genetic|Sequence Analysis, DNA|Software Design', 'Journal Article', '10.1093/bioinformatics/17.3.226', '11294788', 'The field of DNA linguistics has emerged from pioneering work in computational linguistics and molecular biology. Most formal grammars in this field are expressed using Definite Clause Grammars but these have computational limitations which must be overcome. The present study provides a new DNA parsing system, comprising a logic grammar formalism called Basic Gene Grammars and a bidirectional chart parser DNA-ChartParser.'),
(69904, 2001, 'bio', 'Flexibility of the genetic code with respect to DNA structure', 'Baisnée, P F|Baldi, P|Brunak, S|Pedersen, A G', 'Department of Information and Computer Science, University of California, Irvine, CA 92697-3425, USA. pfbald@ics.uci.edu|Department of Information and Computer Science, University of California, Irvine, CA 92697-3425, USA. pfbald@ics.uci.edu|Department of Information and Computer Science, University of California, Irvine, CA 92697-3425, USA. pfbald@ics.uci.edu|Department of Information and Computer Science, University of California, Irvine, CA 92697-3425, USA. pfbald@ics.uci.edu', 'United States|United States|United States|United States', 8, 'Amino Acids|Bacterial Proteins|DNA|DNA, Bacterial|Dinucleotide Repeats|Escherichia coli|Evolution, Molecular|Nucleic Acid Conformation|Sequence Analysis, DNA|Trinucleotide Repeats', 'Journal Article', '10.1093/bioinformatics/17.3.237', '11294789', 'The primary function of DNA is to carry genetic information through the genetic code. DNA, however, contains a variety of other signals related, for instance, to reading frame, codon bias, pairwise codon bias, splice sites and transcription regulation, nucleosome positioning and DNA structure. Here we study the relationship between the genetic code and DNA structure and address two questions. First, to which degree does the degeneracy of the genetic code and the acceptable amino acid substitution patterns allow for the superimposition of DNA structural signals to protein coding sequences? Second, is the origin or evolution of the genetic code likely to have been constrained by DNA structure?'),
(69905, 2001, 'bio', 'MetaFam: a unified classification of protein families I Overview and statistics', 'Silverstein, K A|Shoop, E|Johnson, J E|Retzel, E F', 'Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE, Minneapolis, MN 55455-0312, USA.|Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE, Minneapolis, MN 55455-0312, USA.|Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE, Minneapolis, MN 55455-0312, USA.|Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE, Minneapolis, MN 55455-0312, USA.', 'United States|United States|United States|United States', 0, 'Data Interpretation, Statistical|Databases, Factual|Proteins|Sequence Analysis', 'Journal Article', '10.1093/bioinformatics/17.3.249', '11294790', 'Protein sequence classification is becoming an increasingly important means of organizing the voluminous data produced by large-scale genome sequencing projects. At present, there are several independent classification methods. To aid the general classification effort, we have created a unified protein family resource, MetaFam. MetaFam is a protein family classification built upon 10 publicly-accessible protein family databases (Blocks + DOMO, Pfam, PIR-ALN, PRINTS, PROSITE, ProDom, PROTOMAP, SBASE, and SYSTERS). MetaFams family supersets, as we call them, are created automatically using set-theory to compare families among the databases. Families of one database are matched to those in another when the intersection of their members exceeds all other possible family pairings between the two databases. Pairwise family matches are drawn together transitively to create a new list of protein family supersets.'),
(69906, 2001, 'bio', 'MetaFam: a unified classification of protein families II Schema and query capabilities', 'Shoop, E|Silverstein, K A|Johnson, J E|Retzel, E F', 'Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE, Minneapolis, MN 55455-0312, USA.|Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE, Minneapolis, MN 55455-0312, USA.|Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE, Minneapolis, MN 55455-0312, USA.|Computational Biology Centers, Academic Health Center, University of Minnesota, Mayo Mail Code 43, 420 Delaware St SE, Minneapolis, MN 55455-0312, USA.', 'United States|United States|United States|United States', 0, 'Databases, Factual|Proteins', 'Journal Article', '10.1093/bioinformatics/17.3.262', '11294791', 'Protein sequence and family data is accumulating at such a rapid rate that state-of-the-art databases and interface tools are required to aid curators with their classifications. We have designed such a system, MetaFam, to facilitate the comparison and integration of public protein sequence and family data. This paper presents the global schema, integration issues, and query capabilities of MetaFam.'),
(69907, 2001, 'bio', 'Picasso: generating a covering set of protein family profiles', 'Heger, A|Holm, L', 'Structural Genomics Group, EMBL-EBI, Cambridge CB10 1SD, UK. heger@embl-ebi.ac.uk|Structural Genomics Group, EMBL-EBI, Cambridge CB10 1SD, UK. heger@embl-ebi.ac.uk', 'United Kingdom|United Kingdom', 54, 'Algorithms|Calibration|Databases, Factual|Proteins|Sequence Alignment', 'Journal Article', '10.1093/bioinformatics/17.3.272', '11294792', 'Evolutionary classification leads to an economical description of protein sequence data because attributes of function and structure are inherited in protein families. This paper presents Picasso, a procedure for deriving a minimal set of protein family profiles that cover all known protein sequences.'),
(69908, 2001, 'bio', 'Genview and Gencode : a pair of programs to test theories of genetic code evolution', 'Ronneberg, T A|Freeland, S J|Landweber, L F', 'Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.|Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.|Department of Ecology and Evolutionary Biology, Princeton University, Princeton, NJ 08544, USA.', 'United States|United States|United States', 4, 'Evolution, Molecular|Proteins|Software', 'Journal Article', '10.1093/bioinformatics/17.3.280', '11294793', 'GENVIEW: and GENCODE: are tools for testing the adaptive nature of a genetic code under different assumptions about patterns of genetic error and the nature of amino acid similarity. GENVIEW: provides a user friendly, point-and-click interface by which a user may reproduce and extend analysis of the adaptive properties of the standard genetic code or any of its secondary derivatives. GENVIEW: is a graphical user interface (GUI) program which runs on Linux, Unix and Microsoft Windows platforms and is based on the GTKf + toolkit. GENVIEW: outputs ASCII configuration files which are interpreted by GENCODE: to perform an analysis. GENCODE: is available for the same platforms as GENVIEW.'),
(69909, 2001, 'bio', 'Clustering of highly homologous sequences to reduce the size of large protein databases', 'Li, W|Jaroszewski, L|Godzik, A', 'San Diego Supercomputer Center, La Jolla, CA 92093, USA. liwz@sdsc.edu|San Diego Supercomputer Center, La Jolla, CA 92093, USA. liwz@sdsc.edu|San Diego Supercomputer Center, La Jolla, CA 92093, USA. liwz@sdsc.edu', 'United States|United States|United States', 0, 'Algorithms|Databases, Factual|Proteins|Sequence Analysis|Software', 'Journal Article', '10.1093/bioinformatics/17.3.282', '11294794', 'We present a fast and flexible program for clustering large protein databases at different sequence identity levels. It takes less than 2 h for the all-against-all sequence comparison and clustering of the non-redundant protein database of over 560,000 sequences on a high-end PC. The output database, including only the representative sequences, can be used for more efficient and sensitive database searches.'),
(69910, 2001, 'bio', 'ASEdb: a database of alanine mutations and their effects on the free energy of binding in protein interactions', 'Thorn, K S|Bogan, A A', 'Graduate Group in Biophysics, University of California, San Francisco, CA 94143, USA. thorn@itsa.ucsf.edu|Graduate Group in Biophysics, University of California, San Francisco, CA 94143, USA. thorn@itsa.ucsf.edu', 'United States|United States', 293, 'Alanine|Databases, Factual|Energy Transfer|Mutagenesis, Site-Directed|Proteins', 'Journal Article', '10.1093/bioinformatics/17.3.284', '11294795', 'The Alanine Scanning Energetics database (ASEdb) is a searchable database of single alanine mutations in protein-protein, protein-nucleic acid, and protein-small molecule interactions for which binding affinities have been experimentally determined. In cases where structures are available, it contains surface areas of the mutated side chain and links to the PDB entries. It is useful for studying the contribution of single amino acids to the energetics of protein interactions, and can be updated by researchers as new data are generated.'),
(69911, 2001, 'bio', 'Dynamic simulation of the human red blood cell metabolic network', 'Jamshidi, N|Edwards, J S|Fahland, T|Church, G M|Palsson, B O', 'Department of Bioengineering, University of California-San Diego, La Jolla, CA 92093, USA.|Department of Bioengineering, University of California-San Diego, La Jolla, CA 92093, USA.|Department of Bioengineering, University of California-San Diego, La Jolla, CA 92093, USA.|Department of Bioengineering, University of California-San Diego, La Jolla, CA 92093, USA.|Department of Bioengineering, University of California-San Diego, La Jolla, CA 92093, USA.', 'United States|United States|United States|United States|United States', 79, 'Computer Simulation|Erythrocytes|Humans|Models, Biological|Software', 'Journal Article', '10.1093/bioinformatics/17.3.286', '11294796', 'We have developed a Mathematica application package to perform dynamic simulations of the red blood cell (RBC) metabolic network. The package relies on, and integrates, many years of mathematical modeling and biochemical work on red blood cell metabolism. The extensive data regarding the red blood cell metabolic network and the previous kinetic analysis of all the individual components makes the human RBC an ideal model system for mathematical metabolic models. The Mathematica package can be used to understand the dynamics and regulatory characteristics of the red blood cell.'),
(69912, 2001, 'bio', 'MEG (Model Extender for Gepasi): a program for the modelling of complex, heterogeneous, cellular systems', 'Mendes, P|Kell, D B', 'Institute of Biological Sciences, University of Wales, Aberystwyth SY23 3DD, UK. mendes@vt.edu|Institute of Biological Sciences, University of Wales, Aberystwyth SY23 3DD, UK. mendes@vt.edu', 'United Kingdom|United Kingdom', 25, 'Computer Simulation|Metabolism|Models, Biological|Software', 'Journal Article', '10.1093/bioinformatics/17.3.288', '11294797', 'We describe a program for the construction of spatially distributed metabolic models, which may then be simulated using the metabolic simulator GEPASI: This is useful for the modelling of heterogeneous systems whether as liquid cultures or as spatially organised systems with specified interconnections.');
