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SSRIT specifications

Information


Unique identifier OMICS_20209
Name SSRIT
Alternative name Simple Sequence Repeat Identification Tool
Interface Web user interface
Restrictions to use None
Input data Some sequences.
Input format FASTA
Programming languages Perl
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline SSRIT Team <>

Information


Unique identifier OMICS_20209
Name SSRIT
Alternative name Simple Sequence Repeat Identification Tool
Software type Pipeline/Workflow
Restrictions to use None
Input data Some sequences.
Input format FASTA
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Stability Stable
Requirements
Netscape or IE.
Maintained Yes

Versioning


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Maintainer


  • person_outline SSRIT Team <>

Publication for Simple Sequence Repeat Identification Tool

SSRIT in pipelines

 (14)
2016
PMCID: 5381562
PMID: 28172771
DOI: 10.1093/gbe/evw271

[…] in . di-, tri- and tetramer single sequence repeats (ssrs) with at least three times repetitions of the core sequence motif were analyzed and counted per species and regions occurring employing ssrit (). the number of forward (tandem) and palindromic (inverted) repeats of at least 12 bp were identified using the tandem repeats finder () and the palindromic sequences finder (), […]

2014
PMCID: 3951189
PMID: 24622329
DOI: 10.1371/journal.pone.0087693

[…] a unigene database consisting of potential alternative splicing transcripts was obtained through the clustering analysis. ssr analysis of the unigenes longer than 1 kb was performed using the ssrit software ., the assembled sequences were searched against the ncbi nr and nt databases (last update was on march 1st, 2011) and swiss-prot database using blastn (version 2.2.14) with an e-value […]

2014
PMCID: 4018402
PMID: 24821410
DOI: 10.1371/journal.pone.0096855

[…] rate calculation. significance cutoffs included a p-value of 0.05 and a minimum of 5 mapping entries per go term., the assemblies of dv92 and g3116 were mined for ssrs using perl code from the simple sequence repeat identification tool (ssrit; ; http://archive.gramene.org/db/markers/ssrtool). we identified di-, tri-, tetra-, penta-, and hexa-nucleotide ssrs with a minimum of 8, 6, 4, 3, […]

2013
PMCID: 3826648
PMID: 24129506
DOI: 10.1038/ncomms3602

[…] short sequence reads from gaiix/hiseq2000 and long reads from roche 454 gs-flx. we identified simple sequence repeats, low complexity dna sequences and satellites from the m. martensii genome using ssrit and repeatmasker (version 3.2.9). putative tes in the m. martensii genome were located using blast search against a scorpion-specific te library constructed by homologue-based method […]

2013
PMCID: 4105024
PMID: 25202551
DOI: 10.3732/apps.1200345

[…] as shown in ). in total, 58 sequences had a microsatellite insert with a dinucleotide of at least seven repeat units or a tetra- or trinucleotide of at least five repeat units, were chosen using the simple sequence repeat identification tool (ssrit; http://www.gramene.org/db/searches/ssrtool) (), and the primer pairs were designed based on the flanking sequences of the microsatellite loci using […]


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SSRIT in publications

 (93)
PMCID: 5941480
PMID: 29739315
DOI: 10.1186/s12863-018-0615-x

[…] and its effect on splicing either as enhancers or silencers []. here, the detection of sres near ssrs in pre-mirnas strongly suggests the possible involvement of ssrs in shaping episodes of as., the ssrit analysis of all the available mirna precursors extracted from mirbase showed significant presence of ssrs which accounted to about 29.8%. the frequency and distribution pattern of ssrs varied […]

PMCID: 5738344
PMID: 29263338
DOI: 10.1038/s41598-017-18049-8

[…] that the information is unknown. , note: “—” indicates that the information is unknown., note: “—” indicated that the information is unknown., ssrs were detected in the assembled unigenes using the simple sequence repeat identification tool program (microsatellite), and the ssrs were considered to contain mono-, di-, tri-, tetra-, penta-, and hexa-nucleotides with minimum repeat numbers of ten, […]

PMCID: 5731681
PMID: 29244864
DOI: 10.1371/journal.pone.0189781

[…] function with little variation in expression levels []., identification of di-, tri-, tetra-, penta-, and hexanucleotide ssr loci, with a minimum repeat numbers of two was performed using the simple sequence repeat identification tool (ssrit, http://archive.gramene.org/db/markers/ssrtool)., we acknowledge the excellent technical assistance of melinda dornbusch and susan miller in plant […]

PMCID: 5555463
PMID: 28592558
DOI: 10.1534/g3.117.043943

[…] o. nivara that were involved in pollen sterility in the t65 genetic background (table s1 in file s2). three pairs of primers for ssr markers wgs76, wgs1, and wg1 were newly designed in this study in ssrit software (). five ssr markers (rm471 and rm1359 on chromosome 4 and rm6652, rm1353, and rm6081 on chromosome 7) were used for linkage analysis in the bc4f3 population (table s1 in file s2). […]

PMCID: 5499747
PMID: 28505302
DOI: 10.1093/gbe/evx096

[…] libraries representing known repeats (). de novo repeat identification and modeling were finished by repeat finding program, repeatmodeler v1.0.8 (). ssrs were identified by using perl script on simple sequence repeat identification tool (ssrit) (ftp://ftp.gramene.org/pub/gramene/archives/software/scripts/ssr.pl) in the r. philippinarum genome. ssr target primer pairs were designed […]


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SSRIT institution(s)
Department of Plant Breeding, USDA-ARS Center for Agricultural Bioinformatics, Cornell University, Ithaca, NY, USA; Department of Molecular Biotechnology, University of Washington, Seattle, WA, USA
SSRIT funding source(s)
Supported by the Rockefeller Foundation for financial support (RF98001#663 and RF99001#726).

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