Comparison of Genomic DNA to cDNA Alignment Methods

Miguel GalvesZanoni Dias

Aligning cDNA sequences to genomic sequences is a very common way to study expressed sequences, find their genes, and study alternative splicing. Several computer programs address this problem, using heuristics to define exon regions. Usually, standard alignment algorithms are not used to align ESTs to genomic DNA, due to the existence of large regions of introns. This paper compares the EST-to-genomic alignments produced by sim4, est genome, Spidey and standard sequence aligners using an appropriate score. Surprisingly, standard aligners performed quite well with sequences having few errors.

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