RALP 1.11
:: DESCRIPTION
RALP calculates the statistical parameters in the modified Gumbel distribution for repeats.
::DEVELOPER
:: SCREENSHOTS
Command Line
:: REQUIREMENTS
- Linux / Windows
:: DOWNLOAD
:: MORE INFORMATION
Tag: Repeat
RISCI – Repeat Induced Sequence Change Identifier
RISCI
:: DESCRIPTION
RISCI (Repeat Induced Sequence Changes Identifier) is a comprehensive, comparative genomics based, in silico subtractive hybridization tool, to identify differential insertions and associated subtle sequence changes like target site duplications (TSD), 3’ and 5′ flank transductions, insertion mediated deletions, recombination mediated deletions and polymorphism induced by transposons. Post insertion changes such as recombination mediated deletions and disruptions are also picked up by RISCI. It emulates subtractive hybridization in the sense that, only when the locus in the genomes is differential, does it report the sequence changes associated with the transposon insertion.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2010 Dec 26;11:609. doi: 10.1186/1471-2105-11-609.
RISCI–Repeat Induced Sequence Changes Identifier: a comprehensive, comparative genomics-based, in silico subtractive hybridization pipeline to identify repeat induced sequence changes in closely related genomes.
Singh V1, Mishra RK.
RepeatSeq v0.8.2 – Genotyping Microsatellite Repeats Tool
RepeatSeq v0.8.2
:: DESCRIPTION
RepeatSeq determines genotypes for microsatellite repeats in high-throughput sequencing data.
:: DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux/ Windows
- Python
:: DOWNLOAD
:: MORE INFORMATION
Citation
Nucleic Acids Res. 2013 Jan 7;41(1):e32. doi: 10.1093/nar/gks981. Epub 2012 Oct 22.
Accurate human microsatellite genotypes from high-throughput resequencing data using informed error profiles.
Highnam G1, Franck C, Martin A, Stephens C, Puthige A, Mittelman D.
TRhist 1.0.1 – Tandem Repeat Profiler in Personal Genomes
TRhist 1.0.1
:: DESCRIPTION
TRhist is a tool for finding significat tandem repeats using short reads.
::DEVELOPER
Morishita Laboratory, the University of Tokyo
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux / Windows
- JRE
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2014 Mar 15;30(6):815-22. doi: 10.1093/bioinformatics/btt647. Epub 2013 Nov 8.
Rapid detection of expanded short tandem repeats in personal genomics using hybrid sequencing.
Doi K1, Monjo T, Hoang PH, Yoshimura J, Yurino H, Mitsui J, Ishiura H, Takahashi Y, Ichikawa Y, Goto J, Tsuji S, Morishita S.
TRAL 2.0 – Tandem Repeat Annotation Library
TRAL 2.0
:: DESCRIPTION
TRAL makes annotation of tandem repeats in amino acid and nucleic data simple. TRAL includes modules for detecting tandem repeats with both de novo software and sequence profile HMMs; statistical significance analysis of putative tandem repeats, and filtering of redundant predictions.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux/MacOsX
- Python
:: DOWNLOAD
:: MORE INFORMATION
Citation
TRAL: Tandem repeat annotation library.
Schaper E, Korsunsky A, Messina A, Murri R, Pečerska J, Stockinger H, Zoller S, Xenarios I, Anisimova M.
Bioinformatics. 2015 May 18. pii: btv306.
msatcommander 1.0.8 – Locate Microsatellite Repeats, Design Locus-specific Primers, and Tag ’em
msatcommander 1.0.8
:: DESCRIPTION
msatcommander is a python program written to locate microsatellite (SSR, VNTR, &c) repeats within fasta-formatted sequence or consensus files. msatcommander will search for all di-, tri-, tetra-, penta-, and hexa-nucleotide repeats (with options to search for fewer repeat types and combinations of repeat types).
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
- MacOsX/Windows
- Python
:: DOWNLOAD
:: MORE INFORMATION
Citation
msatcommander: detection of microsatellite repeat arrays and automated, locus-specific primer design.
Faircloth BC.
Mol Ecol Resour. 2008 Jan;8(1):92-4. doi: 10.1111/j.1471-8286.2007.01884.x.
RepeatAround 2.1 – Find Repeats in Circular Genomes
RepeatAround 2.1
:: DESCRIPTION
RepeatAround is a Windows based software tool designed to find “direct repeats”, “inverted repeats”, “mirror repeats” and “complementary repeats”, from 3 bp to 64 bp length, in circular genomes. It processes input files directly extracted from GenBank database and several genomes can be input simultaneously. The program provides visualisation of the repeats location in the genomic structure and the search for specific motifs is also possible. Outputs can be obtained in a spreadsheet containing information on the number and location of the repeats. The software also generates random circular genomes, for statistical evaluations or comparisons between observed and expected repeats distributions.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
- Windows
:: DOWNLOAD
:: MORE INFORMATION
Citation
Goios A, Meirinhos J, Rocha R, Lopes R, Amorim A, Pereira L.
RepeatAround: A software tool for finding and visualizing repeats in circular genomes and its application to a human mtDNA database.
Mitochondrion. 2006 6: 218-224.
aPPRove – Accurate Prediction of RNA and Pentatricopeptide Repeat Protein Binding
aPPRove
:: DESCRIPTION
aPPRove is a computational tool that predicts the interaction of a PPR with its RNA binding site.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Web browser
:: DOWNLOAD
:: MORE INFORMATION
Citation
New Phytol. 2011 Jul;191(1):37-47. doi: 10.1111/j.1469-8137.2011.03746.x. Epub 2011 May 9.
The evolution of RNA editing and pentatricopeptide repeat genes.
Fujii S1, Small I.
CRISPRdigger 1.007 – Detecting CRISPRs with better direct Repeat Annotations
CRISPRdigger 1.007
:: DESCRIPTION
CRISPRdigger is a de novo CRISPR detection program which could identify more truncated DR and has higher accuracy and more contents in the test genomes compared with the present other tools-CRISPRFinder[1], CRT[2] and PILER-CR[3].
::DEVELOPER
Health Informatics Lab (HILab)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Linux/ MacOsX
- Perl
:: DOWNLOAD
:: MORE INFORMATION
Citation
Sci Rep. 2016 Sep 6;6:32942. doi: 10.1038/srep32942.
CRISPRdigger: detecting CRISPRs with better direct repeat annotations.
Ge R, Mai G, Wang P, Zhou M, Luo Y, Cai Y, Zhou F
WDRR – WD40 Repeat Recognition
WDRR
:: DESCRIPTION
WDRR is a new WD40 Repeat Recognition method, which uses predicted secondary structure information to generate candidate repeat segments, and further employs a profile-profile alignment to identify the correct WD40 repeats from candidate segments.
::DEVELOPER
Ziding Zhang’s Lab, China Agricultural University
:: SCREENSHOTS
N/A
:: REQUIREMENTS
- Web Server
- PHP
:: DOWNLOAD
:: MORE INFORMATION
Citation
J Theor Biol. 2016 Jun 7;398:122-9. doi: 10.1016/j.jtbi.2016.03.025.
Identification of WD40 repeats by secondary structure-aided profile-profile alignment.
Wang C, Dong X, Han L, Su XD, Zhang Z, Li J, Song J