gmap

Summary

Software Description

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.

General Linux

To load this module for use in a Linux environment, you can run the command:

module load gmap

Depending on where you are working, there may be more than one version of gmap available. To see which modules are available for loading you can run:

module avail gmap