SEPON, Selection and Evaluation Pipeline for OligoNucleotide generates n-mer oligonucleotide sequences from expressed sequence tags of non-annotated genomes for microarray gene-expression profiling. A non-target melting temperature (T(m)) algorithm will reduce cross-hybridization by estimating T(m) of oligonucleotide hybridization to non-specific targets (non-target T(m)) and discard oligonucleotides with non-target T(m) estimate above user-defined threshold. SEPON allows user-defined filtering, predicts exon location, assigns penalty based on 3 distance, GC content, secondary structure T(m) and non-target T(m) and ranks oligonucleotides for optimal selection.