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- Title
GMAP: a genomic mapping and alignment program for mRNA and EST sequences.
- Authors
Wu, Thomas D; Watanabe, Colin K
- Abstract
We introduce GMAP, a standalone program for mapping and aligning cDNA sequences to a genome. The program maps and aligns a single sequence with minimal startup time and memory requirements, and provides fast batch processing of large sequence sets. The program generates accurate gene structures, even in the presence of substantial polymorphisms and sequence errors, without using probabilistic splice site models. Methodology underlying the program includes a minimal sampling strategy for genomic mapping, oligomer chaining for approximate alignment, sandwich DP for splice site detection, and microexon identification with statistical significance testing.
- Publication
Bioinformatics (Oxford, England), 2005, Vol 21, Issue 9, p1859
- ISSN
1367-4803
- Publication type
Journal Article
- DOI
10.1093/bioinformatics/bti310