msatcommander protocols

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msatcommander specifications

Information


Unique identifier OMICS_16541
Name msatcommander
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Input data The DNA sequence data in single-sequence or concatenated.
Input format FASTA
Output data A summary file, the locus-specific primers.
Output format CSV
Operating system Unix/Linux, Mac OS, Windows
Programming languages Python
License GNU General Public License version 2.0
Computer skills Medium
Version 1.0.8
Stability Stable
Requirements
BioPython, wxPython
Maintained Yes

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Maintainer


  • person_outline Brant Faircloth <>

Publication for msatcommander

msatcommander in pipelines

 (22)
2018
PMCID: 5819644
PMID: 29463303
DOI: 10.1186/s13104-018-3249-1

[…] of 120 base pair (bp), a match percentage of 94% and a minimum sequence length of 150 bp. from this dataset all di-, tri-, tetra-, penta- and hexanucleotides repeats were screened with the software msatcommander [, ] and sequences less than 100 bp and/or with a small number of repeats were excluded. primers were designed with primerselect software (part of the lasergene package []). every […]

2018
PMCID: 5819644
PMID: 29463303
DOI: 10.1186/s13104-018-3249-1

[…] areas 124 km apart in norway and in sweden (table )., after the titanium 454 sequencing 31037 sequences were obtained, which resulted in 6252 potential microsatellite sequences after screening with msatcommander. sixteen microsatellite nonpalindromic tetranucleotide repeats with lengths between 85 and 226 bp, and with number of repeats between 5 and 15 were selected. blastn analysis […]

2018
PMCID: 5827183
PMID: 29520294
DOI: 10.3389/fgene.2018.00046

[…] code (ec), and kyoto encyclopedia of genes and genomes (kegg) metabolic pathways analysis through the bi-directional best hits (bbh) method., microsatellites were identified in the contigs using msatcommander software (faircloth, ). primers flanking the microsatellite loci were designed with primer3plus software (rozen and skaletsky, ). the six possible reading frames of the consensus […]

2017
PMCID: 5260064
PMID: 28114901
DOI: 10.1186/s12862-017-0878-2

[…] inferred with the mtigs was used to assess cross-amplification and polymorphism of 40 microsatellite loci developed de novo for p. limitata. these were identified in silico by screening with msatcommander [] a genomic dna library (biocant, cantanhede, portugal; http://www.biocant.pt/) using shotgun 454 pyrosequencing. from these, 13 loci were selected to produce multi-locus genotypes […]

2017
PMCID: 5749819
PMID: 29299395
DOI: 10.3732/apps.1700084

[…] de novo assembly was performed using clc genomics workbench (qiagen) and produced 1,920,476 contigs, where parameters were set as: average coverage value of 25× and minimum contig length of 299 bp. msatcommander 1.0.8 software was used to identify contigs carrying di-, tri-, and tetranucleotide repeats with a minimum of five repeats and a minimum tract length of 100 bp (other parameters […]


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msatcommander in publications

 (101)
PMCID: 5885378
PMID: 29618324
DOI: 10.1186/s12864-018-4633-x

[…] chloroplast genomes using the online reputer software with a minimum repeat size of 30 bp and sequence identity greater than 90% []. chloroplast simple sequence repeats (cpssrs) were detected using msatcommander v0.8.2 [] with a threshold ten, five, five, three, three, and three repeat units for mono-, di-, tri-, tetra-, penta-, and hexanucleotide ssrs, respectively., multiple alignments […]

PMCID: 5870918
PMID: 29587859
DOI: 10.1186/s13104-018-3301-1

[…] pgm system with each species allocated approximately 25% of a 318 chip. raw genomic data were converted to fasta format using geneious ver. 8.1 []. microsatellite motifs were identified using msatcommander 1.0.8 []. parameters were set to search for perfect tri- and tetranucleotide repeats with a minimum length of eight repeat units to decrease the potential for genotyping errors due […]

PMCID: 5855144
PMID: 29593777
DOI: 10.3389/fgene.2018.00073

[…] previously generated by shotgun genome sequencing of p. costatus and deposited in the database of the laboratory of biotechnology and molecular markers were used for in silico analysis. the software msatcommander () was used to identify microsatellite regions. over 100,000 contigs containing microsatellite regions were identified, and about 1,000 primer pairs suggested. we screened the primer […]

PMCID: 5827183
PMID: 29520294
DOI: 10.3389/fgene.2018.00046

[…] code (ec), and kyoto encyclopedia of genes and genomes (kegg) metabolic pathways analysis through the bi-directional best hits (bbh) method., microsatellites were identified in the contigs using msatcommander software (faircloth, ). primers flanking the microsatellite loci were designed with primer3plus software (rozen and skaletsky, ). the six possible reading frames of the consensus […]

PMCID: 5650168
PMID: 29053730
DOI: 10.1371/journal.pone.0186866

[…] sequencing employed the 454 gs flx titanium sequencing kit xl+ (roche) run on ½ 70 x 75 mm picotiter plate., to identify 454 fragments that contained potentially amplifiable loci (pals), we used msatcommander 1.0.8 [] to scan for repeat containing fragments. when running these searches, we required that dinucleotide and trinucleotide motifs contain ≥ eight repeat units […]


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msatcommander institution(s)
D. B. Warnell School of Forestry and Natural Resources, The University of Georgia, Athens, GA, USA
msatcommander funding source(s)
Supported by the Tall Timbers Research Station and Land Conservancy’s Quail Research Initiative, Daniel B. Warnell School of Forestry and Natural Resources, UGA, McIntyre-Stennis projects GEO-0100-MS and GEO-0136-MS, and the UGA Institute of Ecology.

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