SSRIT statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SSRIT
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Tool usage distribution map

This map represents all the scientific publications referring to SSRIT per scientific context
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Associated diseases

This word cloud represents SSRIT usage per disease context
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Protocols

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


No version available

Maintainer


  • person_outline SSRIT Team

Publication for Simple Sequence Repeat Identification Tool

SSRIT citations

 (110)
library_books

A deeper view into the significance of simple sequence repeats in pre miRNAs provides clues for its possible roles in determining the function of microRNAs

2018
BMC Genet
PMCID: 5941480
PMID: 29739315
DOI: 10.1186/s12863-018-0615-x

[…] 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 ex […]

library_books

Cross species transferability of EST SSR markers developed from the transcriptome of Melilotus and their application to population genetics research

2017
Sci Rep
PMCID: 5738344
PMID: 29263338
DOI: 10.1038/s41598-017-18049-8

[…] 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, […]

library_books

Resistant and susceptible responses in alfalfa (Medicago sativa) to bacterial stem blight caused by Pseudomonas syringae pv. syringae

2017
PLoS One
PMCID: 5731681
PMID: 29244864
DOI: 10.1371/journal.pone.0189781

[…] 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). […]

library_books

DNA sampling from eggshells and microsatellite genotyping in rare tropical birds: Case study on Brazilian Merganser

2017
Genet Mol Biol
PMCID: 5738623
PMID: 28981560
DOI: 10.1590/1678-4685-GMB-2016-0297

[…] r long-term storage at −80 °C. Ninety-six clones containing an insert were sequenced using a MEGABACE 1000 automated sequencer (GE Healthcare Life Sciences). Microsatellites were identified using the Simple Sequence Repeat Identification Tool ().Primers were designed for 18 loci containing microsatellites using Primer3Plus software (). An M13 tail was added to the forward primer of each primer pai […]

library_books

Duplication and Loss of Function of Genes Encoding RNA Polymerase III Subunit C4 Causes Hybrid Incompatibility in Rice

2017
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). Tota […]

library_books

The Whole Genome and Transcriptome of the Manila Clam (Ruditapes philippinarum)

2017
Genome Biol Evol
PMCID: 5499747
PMID: 28505302
DOI: 10.1093/gbe/evx096

[…] base 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 with flank […]


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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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