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MISA computational protocol

MISA specifications

Information


Unique identifier OMICS_00110
Name MISA
Alternative names MIcroSAtellite identification tool, MISA-web
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Uwe Scholz <>
  • person_outline Thoma Thiel <>

Information


Unique identifier OMICS_00110
Name MISA
Alternative names MIcroSAtellite identification tool, MISA-web
Interface Web user interface
Restrictions to use None
Input data Accession number(s), sequence
Input format FASTA
Stability Stable
Maintained Yes

Maintainers


  • person_outline Uwe Scholz <>
  • person_outline Thoma Thiel <>

Publications for MIcroSAtellite identification tool

MISA IN pipelines

 (7)
2017
PMCID: 5456083
PMID: 28575007
DOI: 10.1371/journal.pone.0178402

[…] the plastid chromosome was generated using genomevx [22], §jansen [23], # olmstead & sweere [24]., potential ssr markers were detected in the scaffolds of the assembled nuclear genome using the misa tool [25]. we searched for ssrs with motifs ranging from di- to hexa-nucleotides. the minimum number of repeat units was set as following: ten for di-, eight for tri-, seven for tetra-, six […]

2016
PMCID: 4780773
PMID: 26949967
DOI: 10.1371/journal.pone.0151074

[…] on 8,330 contig sequences. the sequences are available on the cupuassu restricted databases at http://lbi.cenargen.embrapa.br/cupuacu/. the ests were screened for the presence of ssrs using the misa software [41] according to the following criteria: i) nucleotide motif/minimum number of repeats of 1/10, 2/6, 3/4, 4/2, 4/3, 5/3, 6/5, 7/2, 8/2 and 9/2; and ii) maximum difference between two […]

2016
PMCID: 4784950
PMID: 26960153
DOI: 10.1371/journal.pone.0150548

[…] interactions of genes. first, using blastx with an e-value threshold of 10−5, 33,807 unigene sequences were grouped in 128 kegg pathways., next, we screened the 71,318 est (unigene) sequences using misa software to identify ssr loci. we found 12,886 ssrs in 10,892 sequences; 1673 of the est sequences contained more than one ssr (table 3)., after filtering, 9324 primer pairs were successfully […]

2016
PMCID: 5162099
PMID: 27986076
DOI: 10.1186/s12864-016-3377-8

[…] at least 5% minor allele frequency. the snps discovered on unanchored contigs were checked for their location with respect to exon sequences of genes. similarly, indels and ssrs were detected using microsatellite identification tool (misa v1.0) [60]. minimum unit size cutoffs of eight for a di-, six for a tri-, and four for tetra-, penta-, and hexanucleotide repeats were used to report ssrs. […]

2014
PMCID: 4114786
PMID: 25072156
DOI: 10.1371/journal.pone.0103583

[…] of selected genes obtained from real-time rt-pcr and rna-seq data analysis was determined in r program., c. roseus transcriptome was screened for the presence of microsatellites (ssrs) using misa [61]. the number of repeating units considered in this study was, six for di-nucleotides, and five for tri-, tetra-, penta- and hexa-nucleotides. we did not consider mono-nucleotide repeats […]

MISA institution(s)
Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, Seeland, Germany; KWS Saat SE, Einbeck, Germany; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
MISA funding source(s)
Supported by German Federal Ministry of Education and Research (BMBF) grant FKZ 0315954A in the frame of project TRITEX.

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