GMAP/GSNAP is a widely used tool for alignment of high-throughput sequence data.
See details about GMAP/GSNAP here:
http://research-pub.gene.com/gmap
Here is the referencable peer-reviewed paper:
Thomas D. Wu and Colin K. Watanabe
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Bioinformatics 2005 21:1859-1875
PUBMED ID 15728110 full citation at http://www.ncbi.nlm.nih.gov/pubmed/15728110
Signed-off-by: Adam Vandenberg <flangy@gmail.com>
Jack Nagel
Angel Pizarro