MatrixCatch 2.7 – Recognition of Composite Regulatory Elements in Promoters

MatrixCatch 2.7

:: DESCRIPTION

MatrixCatch (MCatch) is a tool designed to search for potential composite elements (CEs) in DNA sequences.

::DEVELOPER

MatrixCatch team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 8;14:241. doi: 10.1186/1471-2105-14-241.
MatrixCatch–a novel tool for the recognition of composite regulatory elements in promoters.
Deyneko IV, Kel AE, Kel-Margoulis OV, Deineko EV, Wingender E, Weiss S.

CoMoFinder – Identify Composite Network Motifs in Genome-scale Co-regulatory Networks

CoMoFinder

:: DESCRIPTION

CoMoFinder strives to discover reliable composite network motifs in co-regulatory networks which consist of microRNAs, transcriptional regulators and genes.

::DEVELOPER

Yue Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • JDK

:: DOWNLOAD

 CoMoFinder

:: MORE INFORMATION

Citation:

A novel motif-discovery algorithm to identify co-regulatory motifs in large transcription factor and microRNA co-regulatory networks in human.
Liang C, Li Y, Luo J, Zhang Z.
Bioinformatics. 2015 Mar 18. pii: btv159

ssw2pop – Programs for Simulation and Composite Likelihood Snalysis of Selective Sweep

ssw2pop

:: DESCRIPTION

ssw2pop simulates a joint sample of DNA sequences from two subpopulations that share their ancestral population.

::DEVELOPER

the INNAN Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/MacOsX
  • C Compiler

:: DOWNLOAD

 ssw2pop

:: MORE INFORMATION

Citation

Hideki Innan and Yuseob Kim 2008
Detecting Local Adaptation Using the Joint Sampling of Polymorphism Data in the Parental and Derived Populations
Genetics 179: 1713-172

Compo – Composite Motif Discovery

Compo

:: DESCRIPTION

Compo is a software for composite motif discovery using discrete models.

::DEVELOPER

Geir Kjetil Sandve (geirksa@ifi.uio.no), Bioinformatics & Gene Regulation

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

Compo

:: MORE INFORMATION

miRComp – Composite MicroRNA Target Prediction

miRComp

:: DESCRIPTION

miRComp is a filtering step of putative microRNA targets through aggregating the predictions by several algorithms using two composite statistics – composite ranks and composite “p-values”

::DEVELOPER

Statistical Genetics and Bioinformatics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 miRComp

:: MORE INFORMATION

Citation

Jin Zhou, Shili Lin, Vince Melfi, Joe Verducci (2006).
Composite MicroRNA Target Predictions and Comparisons of Several Prediction Algorithms.
MBI Technical Report No. 51.