Trace chromatogram data of EST sequences in Unigene were processed with PHRED. To identify likely SNPs, single base mismatches were reported from multiple sequence alignments produced by the programs PHRAP, BRO and POA for each Unigene cluster. BRO
corrected possible misreported EST orientations, while POA identified and analyzed non-linear alignment structures indicative of gene mixing/chimeras that might produce spurious SNPs. Bayesian inference was used to weigh evidence for true polymorphi
sm versus sequencing error, misalignment or ambiguity, misclustering or chimeric EST sequences, assessing data such as raw chromatogram height, sharpness, overlap and spacing; sequencing error rates; context-sensitivity; cDNA library origin etc.