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Bioinformatics Advance Access originally published online on February 22, 2005
Bioinformatics 2005 21(9):1859-1875; doi:10.1093/bioinformatics/bti310
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

GMAP: a genomic mapping and alignment program for mRNA and EST sequences

Thomas D. Wu 1,* and Colin K. Watanabe 2

1Department of Bioinformatics Genentech, Inc., South San Francisco, CA 94080, USA
2Department of Corporate Information Technology Genentech, Inc., South San Francisco, CA 94080, USA

*To whom correspondence should be addressed.

Motivation: 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.

Results: On a set of human messenger RNAs with random mutations at a 1 and 3% rate, GMAP identified all splice sites accurately in over 99.3% of the sequences, which was one-tenth the error rate of existing programs. On a large set of human expressed sequence tags, GMAP provided higher-quality alignments more often than BLAT did. On a set of Arabidopsis cDNAs, GMAP performed comparably with GeneSeqer. In these experiments, GMAP demonstrated a several-fold increase in speed over existing programs.

Availability: Source code for GMAP and associated programs is available at http://www.gene.com/share/gmap

Contact: twu{at}gene.com

Supplementary information: http://www.gene.com/share/gmap


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