Bioinformatics Links Directory : Gene Regulation

This section contains links to tools and resources for predicting gene regulation, such as promoter analysis.

PredictRegulon - (Found July 2, 2008 )

PredictRegulon is a tool that, for a given regulatory protein and prokaryotic genome, predicts binding sites and operons. The user selects a prokaryote genome and provides an ungapped multiple sequence alignment representing the binding site. PredictRegulon reports back with predicted binding sites and downstream co-regulated genes.
http://www.cdfd.org.in/predictregulon/

Riboswitch finder - (Found July 2, 2008 )

RNA motif search program that identifies RNA motifs called riboswitches which are metabolic binding domains in mRNA that regulate gene expression. The program was originally designed around a set of riboswitches found in Bacillus subtilis.
http://riboswitch.bioapps.biozentrum.uni-wuerzburg.de/server.html

rMotif - (Found July 2, 2008 )

rMotif provides tools for the discovery of de-novo, fully, or partially characterized regulatory motifs including transcription factor binding sites (TFBS).
http://bioportal.weizmann.ac.il/~lapidotm/rMotif/html/

Target Explorer - (Found July 2, 2008 )

Target Explorer can be used to create custom matrices to describe transcription factor binding sites (TFBS), search for clusters of TFBS, and identify target genes. Free registration is required.
http://trantor.bioc.columbia.edu/Target_Explorer/

TOUCAN 2 - (Found July 2, 2008 )

TOUCAN 2 is a regulatory sequence analysis workbench for Metazoan sequences, directly linked with the Ensembl database and implementing SOAP clients for diverse alignment and motif detection algorithms.
http://www.esat.kuleuven.ac.be/~saerts/software/toucan.php

TraFaC - (Found July 2, 2008 )

TraFaC (Transcription Factor Binding Site Comparison) is a tool that identifes regulatory regions using a comparative sequence analysis approach.
http://trafac.cchmc.org/trafac/index.jsp

TRANSFAC - (Found July 2, 2008 )

Transcription Factor Database of eukaryotic cis-acting regulatory DNA elements and trans-acting factors; free for non-commercial use.
http://www.gene-regulation.com/pub/databases.html#transfac

VOMBAT - (Found July 2, 2008 )

VOMBAT predicts transcription factor binding sites (TFBS) and other motifs in sequence data based on Variable Order Markov models and variable order BAyesian Trees.
http://pdw-24.ipk-gatersleben.de:8080/VOMBAT/

Web Weeder - (Found July 2, 2008 )

Server which identifies conserved motifs within sets of related regulatory DNA sequences, which are likely to be transcription factor binding sites. The interface will automatically conduct several runs using different parameters and output a summary.
http://www.pesolelab.it/

WebMOTIFS - (Found July 2, 2008 )

WebMOTIFS is a tool for motif discovery, scoring, analysis, and visualization. It allows you to use different programs (AlignACE, MDscan, MEME, and Weeder) to search for DNA-sequence motifs, and evaluate the results.
http://fraenkel.mit.edu/webmotifs/