GMATo protocols

View GMATo computational protocol

GMATo statistics

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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

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Documentation


Maintainer


  • person_outline Xuewen Wang <>

Additional information


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

Publication for Genome-wide Microsatellite Analyzing Tool

GMATo in pipelines

 (2)
2017
PMCID: 5587035
PMID: 28876418
DOI: 10.1590/S1678-9946201759066

[…] submitted sequences for rdna as a universal genomic marker for species identification were collected according to the ncbi nucleotides database. to predict potential microsatellite regions, we used gmato v1.2, as a novel software for faster and accurate microsatellite mining at any length., we have designed three primer sets (position 1-223, position 500-700 and position 700-1008) by primer3 […]

2016
PMCID: 4959724
PMID: 27454301
DOI: 10.1371/journal.pone.0159437

[…] with at least 200 bp were maintained for marker identification and functional analysis. ssr motifs with a maximum of 4-nucleotide repeats were identified from the reference file using the software gmato [] with a minimum repeat value of 5. we specifically searched for only di-, tri-, and tetra-nucleotide repeats due to their abundance in plant genomes [–] and excluded other nucleotide repeats […]


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GMATo in publications

 (10)
PMCID: 5823453
PMID: 29470549
DOI: 10.1371/journal.pone.0193316

[…] 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 […]

PMCID: 5798402
PMID: 29416956
DOI: 10.7717/peerj.4350

[…] a circular genome map was drawn using the cgview server (; http://stothard.afns.ualberta.ca/cgview_server)., simple sequence repeats (ssrs) were detected and located in the mg of m. elongata using gmato v1.2 software ()., phylogenetic reconstruction was conducted by selecting only functional protein-coding sequences (cds) present in mgs of all bryophytes under investigation. a total of 33 […]

PMCID: 5732391
PMID: 29246263
DOI: 10.1186/s13104-017-3077-8

[…] ndhd, while the acg initiation codon was found only for rpl2., 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 […]

PMCID: 5632729
PMID: 29046685
DOI: 10.3389/fpls.2017.01713

[…] 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., for mutational […]

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

[…] 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 […]


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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.