Department of Computer Science, Stony Brook, NY, USA.|IBM T.J. Watson Research Center, Yorktown Heights, NY, USA.|IBM T.J. Watson Research Center, Yorktown Heights, NY, USA.|European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Hinxton, Cambridgeshire, UK.|Institute of Immunology, University of Rostock, Rostock, Germany.|Institute of Immunology, University of Rostock, Rostock, Germany.|Gesellschaft für Individualisierte Medizin (IndyMed) mbH, Rostock, Germany.|Department of Intelligent Systems, Jožef Stefan Institute, Ljubljana, Slovenia.|Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy.|Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy.|Department of Electrical, Computer and Biomedical Engineering, University of Pavia, Pavia, Italy.|Institute of Immunology, University of Rostock, Rostock, Germany.|IBM T.J. Watson Research Center, Yorktown Heights, NY, USA.|Computational Biology Department, School of Computer Science, Carnegie Mellon University, Pittsburgh, PA, USA. carlk@cs.cmu.edu.