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 (CBDM) Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
Web Server

:: DOWNLOAD

ARD2

:: 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.

RADAR 1.1.5 – Rapid Automatic Detection and Alignment of Repeats in protein sequences

RADAR 1.1.5

:: DESCRIPTION

RADAR identifies gapped approximate repeats and complex repeat architectures involving many different types of repeats.

::DEVELOPER

European Bioinformatics Institute

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
C++ Compiler
Python

:: DOWNLOAD

RADAR

:: MORE INFORMATION

Citation:

Rapid automatic detection and alignment of repeats in protein sequences. (2000)
Heger A. and Holm L.
Proteins 41(2): 224-237.

M-GCAT 2.0 beta – Detect Highly Conserved Regions in Multiple Genomes with Rearrangements and Repeats

M-GCAT 2.0 beta

:: DESCRIPTION

M-GCAT is a tool for rapidly visualizing and aligning the most highly conserved regions in multiple (typically prokaryote) genomes. M-GCAT is based upon a highly efficient approach to anchor-based multiple genome comparison using a compressed suffix graph and thus can construct multiple genome alignment frameworks in closely related species usually in a few minutes. A couple of important limitations include (1) input sequences MUST be assembled, and (2) the comparison is reference-sequence biased.

::DEVELOPER

the Algorithmics and Genetics Group

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows/ MacOsX
Python

:: DOWNLOAD

M-GCAT

:: MORE INFORMATION

Citation

T. Treangen and X. Messeguer.
M-GCAT: Interactively and efficiently constructing large-scale multiple genome comparison frameworks in closely related species.
BMC Bioinformatics 2006, 7:433.

STAR – Search for Tandem Approximate Repeats

STAR

:: DESCRIPTION

The program STAR (Search for Tandem Approximate Repeats) searches for significant Approximate Tandem Repeats (ATR) of a given motif in a DNA sequence. For each region of the sequence that is similar to a tandem repeat of the input motif, STAR returns a description of the segment that it calls a “Zone”, and an optimal alignment of the zone with the best possible Exact Tandem Repeat. (Here, exact means perfect.) STAR optimally detects all such zones in the sequence.

::DEVELOPER

Olivier Delgrange , Eric Rivals

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux / Mac OsX

:: DOWNLOAD

STAR

:: MORE INFORMATION

Citation

“STAR: an algorithm to Search for Tandem Approximate Repeats.”
Delgrange O. and Rivals E.
Bioinformatics. 2004 20(16):2812-2820.

SearchRepeats – Detection of Exact Repeats by a Compression Algorithm

SearchRepeats

:: DESCRIPTION

SearchRepeats searches for exact non overlapping repeats in nucleotidic (DNA) sequences and outputs these repeats in a text report.

::DEVELOPER

Eric Rivals

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Sun Solaris

:: DOWNLOAD

SearchRepeats

:: MORE INFORMATION

Citation

Fast Discerning Repeats in DNA Sequences with a Compression Algorithm
Rivals, M. Dauchet, J-P. Delahaye, O. Delgrange
Extended abstract in the 8th Workshop on Genome and Informatics (GIW97)
Tokyo, 12-13 Dec 1997

REPRO – Protein Repeats Analysis

REPRO

:: DESCRIPTION

REPRO (Protein Repeats Analysis) is able to recognise distant repeats in a single query sequence. The technique relies on a variation of the Smith-Waterman local alignment strategy to find non-overlapping top-scoring local alignments, followed by a graph-based iterative clustering procedure to delineate the repeat set(s) based on consistency of the pairwise top-alignments.

::DEVELOPER

The Centre for Integrative Bioinformatics VU

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

REPRO

:: MORE INFORMATION

Citation

George RA. and Heringa J. (2000)
The REPRO server: finding protein internal sequence repeats through the web
Trends Biochem. Sci. 25, 515-517.

REPFIND 20040309 – Find Clustered, Exact Repeats in Nucleotide Sequences

REPFIND 20040309

:: DESCRIPTION

REPFIND is a program to find clustered, exact repeats in nucleotide sequences. For each repeat cluster that it finds, it calculates a P-value, which indicates the probability of finding such a concentration of that particular repeat just by chance. Of the many possible clusters for each repeated word, REPFIND selects the one with the most significant P-value.

We are using REPFIND to study localization of messenger RNAs. These molecules sometimes contain signals in their 3′ untranslated regions that specify how they are transported in the cell, prior to being translated. This process is essential for establishing body axes in embryogenesis, among other things. The localization signals often appear to consist of repeat clusters that can be detected by REPFIND.

::DEVELOPER

the Center for Advanced Genomic Technology

:: SCREENSHOTS

Command Line

:: REQUIREMENTS

Windows/ Linux / Mac OsX
Perl
DUST

:: DOWNLOAD

REPFIND

:: MORE INFORMATION

REPFIND Online Version

Citation:

JN Betley, MC Frith, JH Graber, S Choo, JO Deshler (2002). A ubiquitous and conserved signal for RNA localization in chordates. Current Biology, 12, 1756-61.