Abstract
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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© 2005 Springer-Verlag Berlin Heidelberg
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Galves, M., Dias, Z. (2005). Comparison of Genomic DNA to cDNA Alignment Methods. In: Setubal, J.C., Verjovski-Almeida, S. (eds) Advances in Bioinformatics and Computational Biology. BSB 2005. Lecture Notes in Computer Science(), vol 3594. Springer, Berlin, Heidelberg. https://doi.org/10.1007/11532323_18
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DOI: https://doi.org/10.1007/11532323_18
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-540-28008-8
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