TRF 4.09 – Tandem Repeats Finder

TRF 4.09

:: DESCRIPTION

TRF (Tandem Repeats Finder) is a program to locate and display tandem repeats in DNA sequences. In order to use the program, the user submits a sequence in FASTA format. There is no need to specify the pattern, the size of the pattern or any other parameter. The output consists of two files: a repeat table file and an alignment file. The repeat table contains information about each repeat, including its location, size, number of copies and nucleotide content. Clicking on the location indices for one of the table entries opens a second web browser that shows an alignment of the copies against a consensus pattern. The program is very fast, analyzing sequences on the order of .5Mb in just a few seconds. Submitted sequences may be of arbitrary length. Repeats with pattern size in the range from 1 to 2000 bases are detected. Sequence information sent to the server is confidential and deleted after program execution.

::DEVELOPER

Gary Benson

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

  TRF

:: MORE INFORMATION

Citation:

G. Benson,
Tandem repeats finder: a program to analyze DNA sequences
Nucleic Acids Research (1999) Vol. 27, No. 2, pp. 573-580.

T-REKS – Identification of Tandem Repeats

T-REKS

:: DESCRIPTION

T-REKS (Tandem Repeats Exploration based on K-means in Sequences) is an algorithm for de novo detection and alignment of repeats in sequences based on K-means algorithm. Minimal length of repeat arrays is 9 for true homorepeats and 14 for other repeats with potential biological meaning.

::DEVELOPER

BiSMM – Structural Bioinformatics and Molecular Modeling

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / Mac OsX
  • Java

:: DOWNLOAD

 T-REKS 

:: MORE INFORMATION

Citation

Bioinformatics. 2009 Oct 15;25(20):2632-8. Epub 2009 Aug 11.
T-REKS: identification of Tandem REpeats in sequences with a K-meanS based algorithm.
Jorda J, Kajava AV.

mreps 2.6 – Detect Tandem Repeats in DNA sequences

mreps 2.6

:: DESCRIPTION

mreps is a flexible and efficient software for identifying serial repeats (usually called tandem repeats) in DNA sequences.

mreps Online

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX

:: DOWNLOAD

 mreps

:: MORE INFORMATION

Citation:

R. Kolpakov, G. Bana, and G. Kucherov,
mreps: efficient and flexible detection of tandem repeats in DNA,
Nucleic Acid Research, 31 (13), July 1 2003, pp 3672-3678.

RepWords 1.1 – Detect Tandem Repeats in FASTA Sequences

RepWords 1.1

:: DESCRIPTION

RepWords detects tandem repeats in FASTA sequences.

::DEVELOPER

Statistical Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows / MacOsX
  • C++ Compiler

:: DOWNLOAD

 RepWords

:: MORE INFORMATION

Citation

Int J Bioinform Res Appl. 2014;10(4):384-408. doi: 10.1504/IJBRA.2014.062991.
Searching for repeats, as an example of using the generalised Ruzzo-Tompa algorithm to find optimal subsequences with gaps.
Spouge JL, Mariño-Ramírez L, Sheetlin SL.

VNTRseek 1.08 – Detect Tandem Repeat Variants in High-throughput Sequencing data

VNTRseek 1.08

:: DESCRIPTION

VNTRseek is a targeted, effient VNTR (Variable Number of Tandem Repeats) detection software which can provide essential information on VNTR occurrence and characteristics of minisatellites.

::DEVELOPER

Laboratry of Bioinformatcis at Boston University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 VNTRseek

:: MORE INFORMATION

Citation

VNTRseek-a computational tool to detect tandem repeat variants in high-throughput sequencing data.
Gelfand Y, Hernandez Y, Loving J, Benson G.
Nucleic Acids Res. 2014 Jul 23. pii: gku642.

ReviSTER 0.1.7 – Revise Misaligned Reads to simple Tandem Repeats

ReviSTER 0.1.7

:: DESCRIPTION

ReviSTER (Revise Simple Tandem repeat Error Reads) is an automated pipeline using a local mapping reference reconstruction method to revise mismapped (mapped to incorrect position) or partially misaligned (mapped to correct position but one of ends misaligned) reads at STR (Simple Tandem Repeat) loci. It takes FASTQ-formatted files, a reference sequence file and a list file containing STR locations as inputs and utilizes BWA as an initial mapping program.

::DEVELOPER

Garner Lab

:: SCREENSHOTS

Command

:: REQUIREMENTS

:: DOWNLOAD

 ReviSTER

 :: MORE INFORMATION

Citation:

Bioinformatics. 2013 Jul 15;29(14):1734-41. doi: 10.1093/bioinformatics/btt277. Epub 2013 May 15.
ReviSTER: an automated pipeline to revise misaligned reads to simple tandem repeats.
Tae H1, McMahon KW, Settlage RE, Bavarva JH, Garner HR.

ComplexTR 1.2.0 – Discovery of Tandem Repeats having Simple and Complex Pattern Structures

ComplexTR 1.2.0

:: DESCRIPTION

ComplexTR is a software to identify and characterize tandem repeats having simple and complex pattern structures including but not limited to

  1. Simple sequence repeats (SSRs)
  2. Variable length tandem repeats (VLTR)
  3. Multi-periodic tandem repeats (MPTR)

::DEVELOPER

Amy M. Hauth

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl
  • C++ Compiler

:: DOWNLOAD

 ComplexTR

:: MORE INFORMATION

Citation

Bioinformatics. 2002;18 Suppl 1:S31-7.
Beyond tandem repeats: complex pattern structures and distant regions of similarity.
Hauth AM, Joseph DA.

TRAP 1.1 – Tandem Repeats Analysis Program

TRAP 1.1

:: DESCRIPTION

TRAP is a Perl program that provides a unified set of analyses for the selection, classification, quantification and automated annotation of tandemly repeated sequences.

::DEVELOPER

TRAP team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TRAP

:: MORE INFORMATION

Citation:

Sobreira, T.J.; Durham, A.M. & Gruber, A. (2006).
TRAP: automated classification, quantification and annotation of tandemly repeated sequences.
Bioinformatics 22(3): 361-362.

PTRStalker – Protein Tandem Repeats Discovery and Visualization

PTRStalker

:: DESCRIPTION

PTRStalker is a new algorithm for ab-initio detection of fuzzy tandem repeats in protein amino acid sequences.

DEVELOPER

the BioAlgo Group

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 PTRStalker

:: MORE INFORMATION

Citation

Ab initio detection of fuzzy amino acid tandem repeats in protein sequences
Marco Pellegrini, M. Elena Renda, Alessio Vecchio
BMC Bioinformatics 2012, Vol. 13(Suppl 3):S8, March 2012.