Introduction
This file documents soft Genome-wide Microsatellite Analyzing Tool (GMATo) graphic and command line application. The program and manual is freely available at http://sourceforge.net/project/GMATo or on contact.
Genome-wide Microsatellite Analyzing Tool (GMATo) is a novel powerful program for faster SSR mining at any length, comprehensive statistical analysis at genome aspect, especially designed for huge genome at any size in Perl and JAVA scripts.
Software GMATo is a better and faster tool for Simple Sequence Repeats (SSR), also called microsatellite, characterization in a huge genome and for facilitating SSR marker designing in genome scale. The program was successfully analyzed 2G Zea mays genome easily using a normal computer with Windows or Mac or Linux system.
Only one input file is required which contains DNA sequences in raw fasta format and output files in tabular format list all SSR loci information and statistical distribution at four biologist interested classifications.
GMATo also has easy and graphical user interface mode in Java and command line mode in Perl, either running in Windows, Linux and Mac etc. platforms with easily customized parameters control for biologists and bio-informatician.
The program consists of format sequence module (formatchunk.pl), SSR search (gssr.pl and gssrtrim.pl) module and statistic module (gsts.pl). Each can run separately. Module GMAT (GMAT.pl or GMAT.jar) integrates all modules.
Last edit: Xuewen Wang 2012-12-25
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Documentation for GMATo
By Dr Xuewen Wang
This file documents soft Genome-wide Microsatellite Analyzing Tool (GMATo) graphic and command line application. The program and manual is freely available at http://sourceforge.net/project/GMATo or on contact.
Genome-wide Microsatellite Analyzing Tool (GMATo) is a novel powerful program for faster SSR mining at any length, comprehensive statistical analysis at genome aspect, especially designed for huge genome at any size in Perl and JAVA scripts.
Software GMATo is a better and faster tool for Simple Sequence Repeats (SSR), also called microsatellite, characterization in a huge genome and for facilitating SSR marker designing in genome scale. The program was successfully analyzed 2G Zea mays genome easily using a normal computer with Windows or Mac or Linux system.
Only one input file is required which contains DNA sequences in raw fasta format and output files in tabular format list all SSR loci information and statistical distribution at four biologist interested classifications.
GMATo also has easy and graphical user interface mode in Java and command line mode in Perl, either running in Windows, Linux and Mac etc. platforms with easily customized parameters control for biologists and bio-informatician.
The program consists of format sequence module (formatchunk.pl), SSR search (gssr.pl and gssrtrim.pl) module and statistic module (gsts.pl). Each can run separately. Module GMAT (GMAT.pl or GMAT.jar) integrates all modules.
Last edit: Xuewen Wang 2012-12-25