gmap
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.
Info
Module Name
gmap
Last Updated On
08/29/2023
Support Level
Secondary Support
Software Access Level
Open Access
Home Page
Documentation
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
Agate Modules
Default
2015-09-29
Other Modules
2012-06-02, 2012-10-31, 2015-09-29, 2016-11-07, 2017-03-17, 2017-06-20, 2018-07-04
Mangi Modules
Default
2015-09-29
Other Modules
2012-06-02, 2012-10-31, 2015-09-29, 2016-11-07, 2017-03-17, 2017-06-20, 2018-07-04
Mesabi Modules
Default
2015-09-29
Other Modules
2012-06-02, 2012-10-31, 2015-09-29, 2016-11-07, 2017-03-17, 2017-06-20, 2018-07-04