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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


No version available

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 citations

 (639)
library_books

Characterization of new microsatellite markers based on the transcriptome sequencing of Clematis finetiana

2018
Hereditas
PMCID: 5952850
PMID: 29785177
DOI: 10.1186/s41065-018-0060-x

[…] In this study, MISA perl script (http://pgrc.ipk-gatersleben.de/misa) was used to detect microsatellites in unigene sequences. A total of 7532 SSRs were recognized from 6337 unigenes (Table ). Di-nucleotides were th […]

library_books

Genome Sequencing and Analysis of the Peanut B Genome Progenitor (Arachis ipaensis)

2018
Front Plant Sci
PMCID: 5943715
PMID: 29774047
DOI: 10.3389/fpls.2018.00604

[…] 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 mot […]

library_books

SSR marker development and intraspecific genetic divergence exploration of Chrysanthemum indicum based on transcriptome analysis

2018
BMC Genomics
PMCID: 5918905
PMID: 29695227
DOI: 10.1186/s12864-018-4702-1

[…] In this study all 42,023 unigenes in the DIWNT transcriptome were scanned by MISA software (Table ), and 2575 SSR markers present in 2302 genes were identified. The top three repeat types were trinucleotide SSRs (1452), dinucleotide SSRs (714) and tetranucleotide SSRs (271), w […]

library_books

The chloroplast genome sequence of bittersweet (Solanum dulcamara): Plastid genome structure evolution in Solanaceae

2018
PLoS One
PMCID: 5919006
PMID: 29694416
DOI: 10.1371/journal.pone.0196069

[…] us. Redundant repeats found entirely within other repeats as well as duplicated parts of tRNAs were pruned. Perfect and compound simple sequence repeats (SSRs) interrupted by 100-bp were located with MISA []. A threshold level of seven was applied to mononucleotide repeats, four to dinucleotide repeats and three to tri-, tetra, penta-, and hexanucleotide repeats. Output files were manually edited […]

library_books

Using SSR HRM to Identify Closely Related Species in Herbal Medicine Products: A Case Study on Licorice

2018
Front Pharmacol
PMCID: 5928318
PMID: 29740326
DOI: 10.3389/fphar.2018.00407

[…] Genome data for G. uralensis was retrieved from the ngs-data-archive. To identify potential SSR markers, the G. uralensis genome sequences were screened using MISA. We searched for loci with di- and trinucleotide motifs of at least eight or seven repeats, respectively, or with five repeat units for tetra-, penta-, and hexanucleotide SSRs. After screening, m […]

library_books

Modular assembly of transposable element arrays by microsatellite targeting in the guayule and rice genomes

2018
BMC Genomics
PMCID: 5907723
PMID: 29673330
DOI: 10.1186/s12864-018-4653-6

[…] n any genome was employed. Entered scaffolds are scanned for repeated sequences (250-800 bp in length, ≥ 20% GC content) defined by TA microsatellite domains (≥ 12 bp in length). The program utilizes MISA to identify microsatellite domains (http://pgrc.ipk-gatersleben.de/misa/misa.html). Software and Users Guide available at: http://probes.pw.usda.gov/Guayule. […]

Citations

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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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