GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences

Links are provided below in parentheses for users who wish to download the files with a command-line tool, like wget.

Program

Source code:

• Current version 2007-09-28 (http://www.gene.com/share/gmap/src/gmap-2007-09-28.tar.gz)
  Major changes:
  • Implemented iit_update and gmap_update to update IIT files to version 2 (introduced in the 2007-07-16 version; see notes in the previous versions page for details), or convert them back to version 1.
  • GMAP can now read from multiple sequence files on the command line, like this: gmap -d gmapdb *.fa
  • Some fixes for special alignment cases, mostly affecting low-identity or cross-species alignment
  • Greatly reduced amounts of pre-allocated memory, which affected computers with low amounts of RAM
  • Get-genome can now access from map files entries with a particular direction or tag
  • Added a pruning step in the mapping stage
  • Fix for a rare divide-by-zero error
  • Fixed reading of input sequences with multiple PC line feeds
  • Turned off sorting of chromosomes in gmap_setup -S mode, which treats each contig as a chromosome
• Previous versions
• If you would like to be notified of new releases of the source code, please send email to Thomas Wu (twu@gene.com).

Pre-built genome databases (Note: these are provided as a convenience; the source code enables you to build your own genome databases):

• Human chromosome 22 (37 MB) (http://www.gene.com/share/gmap/genomes/chr22.tar.gz)
• Arabidopsis thaliana genome (121 MB) (http://www.gene.com/share/gmap/genomes/arath.tar.gz)
• Human genome, NCBI build 35
  • Part 1 (822 MB) (http://www.gene.com/share/gmap/genomes/NHGD_R35-part1.tar.gz)
  • Part 2 (1.9 GB) (http://www.gene.com/share/gmap/genomes/NHGD_R35-part2.tar (no .gz, because it doesn't compress))

Information

README file from the source code distribution. Contains basic usage information.

Software demonstration given at ISMB 2005. Contains various examples of GMAP usage. [Slides]

References:

Thomas D. Wu and Colin K. Watanabe

GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Bioinformatics 2005 21: 1859-1875 [Abstract] [Full Text] doi:10.1093/bioinformatics/bti310 [Manuscript]