GMATo statistics

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Citations per year

Number of citations per year for the bioinformatics software tool GMATo
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Tool usage distribution map

This map represents all the scientific publications referring to GMATo per scientific context
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Associated diseases

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Popular tool citations

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Protocols

GMATo specifications

Information


Unique identifier OMICS_00106
Name GMATo
Alternative name Genome-wide Microsatellite Analyzing Tool
Software type Package/Module
Interface Command line interface, Graphical user interface
Restrictions to use None
Input data A file containing DNA sequence(s).
Input format MULTI FASTA
Output data One formatting report, one file containing SSR loci information and another file containing statistical distribution of SSR.
Output format TSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java, Perl
Computer skills Advanced
Stability Stable
Maintained Yes

Download


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Versioning


No version available

Documentation


Maintainer


  • person_outline Xuewen Wang

Additional information


https://sourceforge.net/p/gmato/wiki/Home/

Publication for Genome-wide Microsatellite Analyzing Tool

GMATo citations

 (15)
library_books

Genome wide identification and analysis of A to I RNA editing events in bovine by transcriptome sequencing

2018
PLoS One
PMCID: 5823453
PMID: 29470549
DOI: 10.1371/journal.pone.0193316

[…] ense gene pairs) were removed. Fourth, simple sequence repeats patterns (SSR [i.e. motifs ranging in length from 1 to 8 nucleotides with a minimum length of pattern of 6 bases]) were identified using GMATo software [] and removed from further analysis. SNVs located in SSR regions were considered as biased with an offset of ±3 bases. Fifth, to exclude potential false positives resulting from poor m […]

call_split

Complete mitochondrial genome sequence of the “copper moss” Mielichhoferia elongata reveals independent nad7 gene functionality loss

2018
PeerJ
PMCID: 5798402
PMID: 29416956
DOI: 10.7717/peerj.4350
call_split See protocol

[…] Simple sequence repeats (SSRs) were detected and located in the MG of M. elongata using GMATo v1.2 software (). […]

library_books

Current trends for customized biomedical software tools

2017
Bioinformation
PMCID: 5767915
PMID: 29379257
DOI: 10.6026/97320630013402

[…] ch and design primers for genotyping based on genomic data. The tool identifies and targets single sequence repeats (SSR) or orthologous/taxa-specific genes for genotyping using multiplex PCR. GMATo (Genome-wide Microsatellite Analyzing Tool) is a freely available novel tool for SSR mining and statistical characterization in genomes at any size []. Che and Wang [] have developed a computer progra […]

library_books

The complete chloroplast genome sequence of Asian Palmyra palm (Borassus flabellifer)

2017
BMC Res Notes
PMCID: 5732391
PMID: 29246263
DOI: 10.1186/s13104-017-3077-8

[…] Identifications of SSRs and repetitive sequences using by REPuter program (under a cut off n ≥ 10 with 100% sequence identities) [] and GMATo v1.2 [] showed that the cp genome contains, in total, 134 SSR loci and 47 large repeat loci (Additional file : Tables S3 and S4). Among the 134 SSRs, 98 and 20 loci are homopolymers and dipolyme […]

call_split

Comparative Analysis of the Complete Plastomes of Apostasia wallichii and Neuwiedia singapureana (Apostasioideae) Reveals Different Evolutionary Dynamics of IR/SSC Boundary among Photosynthetic Orchids

2017
Front Plant Sci
PMCID: 5632729
PMID: 29046685
DOI: 10.3389/fpls.2017.01713
call_split See protocol

[…] ccording to the following conditions: (1) hamming distance of 3, (2) sequence identity ≥90%, and (3) minimum repeat size ≥30 bp. The simple sequence repeat (SSR) elements were detected using the tool GMATo (), and the criteria of the “Min-length” for mononucleotide SSRs, dinucleotide SSRs, and multi-nucleotide SSRs were set to be greater than 8, 5, and 3 units, respectively. […]

library_books

Genome sequencing of the staple food crop white Guinea yam enables the development of a molecular marker for sex determination

2017
BMC Biol
PMCID: 5604175
PMID: 28927400
DOI: 10.1186/s12915-017-0419-x

[…] valuated for use in primer design. Accordingly, 134,101 SSR-containing sequences, excluding those with single base repeats, were identified. The SSR information for these sequences was analyzed using GMATo [] version 1.2 Build 20130106 with the following parameters: m (minimum motif length) = 2, x (maximum motif length) = 10, and r (minimum repeat number) = 10. The necessary information was obtain […]


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GMATo institution(s)
China Tobacco Gene Research Center, Zhengzhou Tobacco Research Institute, Zhengzhou, China

GMATo review

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Tatiana Orli Milkewitz Sandberg

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Desktop
GMATo is a useful tool for generating statistical analyzes, such as the quantification of microsatellites in any DNA sample. I used this tool for that purpose, and then I combined multiple samples and compared the quantities of microsatellites in each.
This tool has a very useful and clear graphical interface, with a perfect windows version. Perfectly what I was looking for. The parameters can be changed easily, the documentation is clear and includes numerous possibilities of applications for the GMATo, not only for identification and quantification of microsatellites in genomic samples. Very accessible, also for the non-bioinformation public. Finally, I would like to adress the fact that the tool is very fast, easy to install and easy to use inside pipelines.