Tag: TFBS

MatCompare 1.3 – Compare Transcription Factor Binding Site (TFBS) position Frequency Matrices (PFMs)

MatCompare 1.3

:: DESCRIPTION

The MatCompare software provides methods for comparing transcription factor binding site (TFBS) position frequency matrices (PFMs). The user has a choice of using the Kullback-Leibler divergence, the chi squared test or the Fisher-Irwin exact test of similarity.

::DEVELOPER

Michael Zhang Computational Biology Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX

:: DOWNLOAD

 MatCompare

:: MORE INFORMATION

Citation:

Dustin E Schones, Pavel Sumazin and Michael Q Zhang
Similarity of position frequency matrices for transcription factor binding sites
Bioinformatics 2005 21(3):307-313; doi:10.1093/bioinformatics/bth480

TFBS 0.7.1 – Perl modules for Transcription Factor Binding Site Detection and Analysis

TFBS 0.7.1

:: DESCRIPTION

TFBS is a set of integrated, object-oriented Perl modules for transcription factor binding site detection and analysis. It implements objects representing specificity profile matrices, binding sites and sets thereof, pattern generators, and pattern database interfaces.

::DEVELOPER

Computational Regulatory Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 TFBS

:: MORE INFORMATION

Citation:

Lenhard B., Wasserman W.W. (2002)
TFBS: Computational framework for transcription factor binding site analysis.
Bioinformatics 18:1135-1136

TFBSTools 1.30.0 – Transcription Factor Binding Site (TFBS) Analysis

TFBSTools 1.30.0

:: DESCRIPTION

TFBSTools is a package for the analysis and manipulation of transcription factor binding sites and transcription factor profile matrices.

::DEVELOPER

Computational Regulatory Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R/BioConductor

:: DOWNLOAD

 TFBSTools

:: MORE INFORMATION

Citation

TFBSTools: an R/Bioconductor package for transcription factor binding site analysis.
Tan G, Lenhard B.
Bioinformatics. 2016 Jan 21. pii: btw024.

rVista 2.0 – Identification of TFBS Conserved in Pairwise Alignments

rVista 2.0

:: DESCRIPTION

The rVISTA tool combines TFBS predictions, sequence comparisons and cluster analysis to identify noncoding DNA regions that are evolutionarily conserved and present in a specific configuration within genomic sequences. The newly developed version 2.0 of the rVISTA tool can process alignments generated by both the zPicture and blastz alignment programs or use pre-computed pairwise alignments of several vertebrate genomes available from the ECR Browser and GALA database.

::DEVELOPER

Ivan Ovcharenko Research Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

rVISTA 2.0: evolutionary analysis of transcription factor binding sites.
Loots GG, Ovcharenko I.
Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W217-21.

PROMO – Detection of Putative Transcription Factor Binding Sites (TFBS) in DNA sequences

PROMO

:: DESCRIPTION

PROMO is a virtual laboratory for the identification of putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. TFBS defined in the TRANSFAC database are used to construct specific binding site weight matrices for TFBS prediction. The user can inspect the result of the search through a graphical interface and downloadable text files.

::DEVELOPER

the Algorithmics and Genetics Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  No

:: MORE INFORMATION

Citation

Xavier Messeguer, Ruth Escudero, Domènec Farré, Oscar Núñez, Javier Martínez, M.Mar Albà.
PROMO: detection of known transcription regulatory elements using species-tailored searches.
Bioinformatics, 18, 2, 333-334, 2002.