GMAP - Genomic Mapping and Alignment Program for mRNA and EST Sequences

GMAP is 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.

To run this software interactively in a Linux environment run the commands:
module load gmap
gmap_build -d <genome> <fasta_files...>
For a complete listing of options, use the command:
gmap_build --help
Other GMAP utilities may be found in the directory
where VER is the version of GMAP you are using.
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