CRISPRdigger 1.003 – Detecting CRISPRs with better direct Repeat Annotations

CRISPRdigger 1.003

:: 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

Fengfeng Zhou

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ MacOsX
  • Perl

:: DOWNLOAD

 CRISPRdigger

:: MORE INFORMATION

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

faircloth-lab

:: SCREENSHOTS

msatcommander

:: REQUIREMENTS

  • MacOsX/Windows
  • Python

:: DOWNLOAD

 msatcommander

:: 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.

ProRepeat – An Integrated Repository for studying Amino Acid Tandem Repeats in Proteins

ProRepeat

:: DESCRIPTION

ProRepeat is an integrated curated repository and analysis platform for in-depth research on the biological characteristics of amino acid tandem repeats.

::DEVELOPER

ProRepeat team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Nucleic Acids Res. 2012 Jan;40(Database issue):D394-9. doi: 10.1093/nar/gkr1019. Epub 2011 Nov 18.
ProRepeat: an integrated repository for studying amino acid tandem repeats in proteins.
Luo H1, Lin K, David A, Nijveen H, Leunissen JA.

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

SEQ Development Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

  NO

:: 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.

TRAL 0.3.5 – Tandem Repeat Annotation Library

TRAL 0.3.5

:: 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

TRAL team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • Python

:: DOWNLOAD

  TRAL

:: 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.

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

Mittelman lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows
  • Python

:: DOWNLOAD

 RepeatSeq

:: 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

 TRhist

:: 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.

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

Rakesh Mishra Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RISCI

:: 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.

RALP 1.11 – Calculation of the Gumbel Parameters for Repeats

RALP 1.11

:: DESCRIPTION

RALP calculates the statistical parameters in the modified Gumbel distribution for repeats.

::DEVELOPER

Spouge Research Group

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 RALP

:: MORE INFORMATION

ARD2 – Alpha-rod Detector

ARD2

:: DESCRIPTION

ARD2 (Alpha-rod Repeat Detector) is an application for the identification of alpha-rod repeats, also defined as alpha-solenoids (HEAT, Armadillo among others) in protein sequences using a neural network.

::DEVELOPER

Computational Biology and Data Mining Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2013 Nov 21;8(11):e79894. doi: 10.1371/journal.pone.0079894. eCollection 2013.
Functional and genomic analyses of alpha-solenoid proteins.
Fournier D1, Palidwor GA, Shcherbinin S, Szengel A, Schaefer MH, Perez-Iratxeta C, Andrade-Navarro MA.