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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

Versioning


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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

 (41)
2018
PMCID: 5766596
PMID: 29330436
DOI: 10.1038/s41598-017-18534-0

[…] to one or more functional databases as its coding sequence (cds). coding regions of unigenes that could not be aligned with any of the functional databases were predicted by estscan v3.0.2. we used misa v1.0 to detect simple sequence repeats (ssrs; also known as microsatellites sequences) in our unigenes, and used gatk v3.4–0 to detect single nucleotide polymorphism (snp) variants among […]

2018
PMCID: 5797776
PMID: 29445389
DOI: 10.3389/fpls.2018.00077

[…] of transcripts, especially abundant transcripts (grabherr et al., ). to avoid redundancy in the datasets, we used cd-hit (http://weizhong-lab.ucsd.edu/cd-hit) to obtain unigene sequences. the microsatellite identification tool (misa, http://pgrc.ipk-gatersleben.de/misa/) was used to identify microsatellites in the unigenes. twelve microsatellite loci containing three-nucleotide motifs […]

2017
PMCID: 5345388
PMID: 28286710
DOI: 10.7717/peerj.3037

[…] the trnascan-se 1.21 program (). the physical maps were drawn using the web tool organellar genome draw (ogdraw) v1.2 ()., ssrs in m. cathayana and m. multicaulis cp genomes were detected using misa () with the minimal repeat number set to 10, 5, 4, 3, 3, and 3 for mono-, di-, tri-, tetra-, penta-, and hexa-nucleotides, respectively. the distribution, nucleotide composition, […]

2017
PMCID: 5357120
PMID: 28337389
DOI: 10.3732/apps.1600104

[…] germany) with a length of 46,547,889 bp, n50 scaffold size of 1478 bp, n90 scaffold size of 1070 bp, and 32.78% gc content. consequently, 3442 microsatellite sequences were identified using the microsatellite identification tool (misa; ). frequencies of each repeat type were classified as follows: di-, tri-, tetra-, penta-, and hexanucleotide repeats of 34.1% (1176 loci), 14.12% (486 loci), […]

2017
PMCID: 5357124
PMID: 28337393
DOI: 10.3732/apps.1600152

[…] these unigenes, the minimal length was 201 bp, the average length was 686 bp, and the n50 value was 1174 bp., to search for ssr motifs containing two to six nucleotides across these unigenes, the misa tool () was applied with the default parameters except that the settings for mononucleotide repeats were removed from analysis. the results showed that 1892 ssrs were detected in 1709 unigenes. […]


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MISA in publications

 (222)
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] the transposable elements (tes) were classified as described without consideration of the gaps in the genome assembly (wicker et al., )., microsatellite (http://pgrc.ipk-gatersleben.de/misa/) was used to mine ssrs in a. ipaensis genome, and primer 3 v3.0 was used for primer design (thiel et al., ; untergasser et al., ). a ssr was defined with at least 6 repeats for di-nucleotide […]

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

[…] has provided considerable resources for ssr mining and ssr marker applications for research and genetic improvements []. a series of bioinformatics tools for ssrs have also been developed, such as misa [], ssr primer [], and ssr locator []. however, these tools have not yet integrated a computational solution for systematic assessment of ssr polymorphic status, thus the detected ssrs still […]

PMCID: 5828123
PMID: 29732246
DOI: 10.1002/aps3.1015

[…] length was 291 bp, with a maximum length of 791 bp. clean reads were deposited in the national center for biotechnology information (ncbi) sequence read archive (accession number srp101615)., the microsatellite identification tool (misa; thiel et al., ) was used to identify reads that contained ssrs. the minimum motif repeat was defined as six for di‐, and five for tri‐, tetra‐, penta‐, […]

PMCID: 5797098
PMID: 29396453
DOI: 10.1038/s41598-018-20181-y

[…] of repetitive dna in which certain dna motifs (ranging in length from 2–13 base pairs) are repeated, typically 5–50 times. transcripts that were >500 bp were selected for ssr analysis using the microsatellite identification tool (misa; http://pgrc.ipk-gatersleben.de/misa/http://pgrc.ipk-gatersleben.de/misa/). misa can identify seven ssr types, namely mononucleotide, dinucleotide, […]

PMCID: 5796262
PMID: 29360746
DOI: 10.3390/ijms19010319

[…] codons except tryptophan and methionine. our result is in line with previous findings of codon usage preference for a/t ending in other land plants [,]., analysis of ssr occurrence using the microsatellite identification tool (misa) detected mono-, di-, tri-, tetra-, penta- and hexa-nucleotides categories of ssrs in the cp genomes of eight ericales. a total of 197 and 159 ssrs were found […]


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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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