Yedomon / GMATA

software GMATA

GMATA

GMATA stands for Genome-wide Microsatellite Analyzing Toward Application. GMATA is an easiest and fastest bioinformatic tool /software for any Simple Sequence Repeats (SSR) analyses, and SSR marker designing, polymorphism screen, and e-mapping in any DNA sequences. GMATA algorithm has been cited wordwide for more than 100 times.

Updates on version 2.2 (come soon)

1. add a new module for masking SSRs for genome annation
2. add a new function for satelite analysing
3. add tools for mining SSRs in 2nd and 3rd genertation reads
4. new interface

Main functions

This is the software GMATA at GitHUB What is software GMATA v2.2 (latest) Genome-wide Microsatellite Analyzing Toward Application (GMATA) is a software for Simple Sequence Repeats (SSR) analyses, and SSR marker designing and mapping in any DNA sequences. It has the following functions:

1. SSR mining; good for all SSRs:microsatellites, satellites, any tadem repeats
2. Statistical analysis and plotting;
3. SSR loci graphic viewing;
4. Marker designing;
5. ploymorphism screen;
6. Electronic mapping and marker transferability investigation. GMATA is accurate, sensitive and fast. It was designed to process large genomic sequence data sets, especially large whole genome sequences. In theory, genomes of any size can be analyzed by GMATA easily. Software GMATA works on sever, desktop or even laptop, and it can run in graphic interface with just clicks or run in command line or in automated pipeline. It is also cross-platform and supports Unix/Linux, Win and Mac. Results from software GMATA can be directly graphically displayed with genome or gene features in Gbrowser and easily integrated with any genomic database.

Citing this software:

GMATA: an integrated software package for genome-scale SSR mining, marker development and viewing X Wang, L Wang Frontiers in Plant Science 7, doi 10.3389/fpls.2016.01350

Alternative downloading link for this software

Sourceforge

Features

Accurate and fastest SSR mining in any large sequences Complete statistical analysis and plotting SSR loci and marker graphic displaying in Gbrowser with genome features Specific SSR marker designing, and simulated PCR Electronic mapping, and marker transferability investigation

Discussion

sourceforge discussion

Testing data

To make a test run: go to web https://sourceforge.net/projects/gmata/files/?source=navbar to download the test data called "datav21.zip" or download the "testseq.fasta" and then put a separately folder e.g. "data" instead of running in the source script, otherwise all lots of results will write to the same directory. Of course, it will run well if you still want to keep running the analysis on "testseq.fasta"" in the installed software directory.