Bioinformatics Links Directory : Gene Regulation

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

Gene Regulation - (Found July 2, 2008 )

Access to databases, programs and papers related to gene regulation.
http://www.gene-regulation.com

Gibbs Motif Sampler - (Found July 2, 2008 )

Gibbs Motif Sampler allows you to identify motifs, conserved regions, in DNA or protein sequences. This tool can be applied for the detection of transcription factor binding sites (TFBS).
http://bayesweb.wadsworth.org/gibbs/gibbs.html

iCR - (Found July 2, 2008 )

Identify Conserved targets of a Regulon (iCR) predicts regulatory binding sites based on conservation across multiple species. The user provides an ungapped multiple sequence alignment representing the regulatory binding site. iCR reports back with predicted binding sites that are conserved and highlights the downstream co-regulated genes.
http://210.212.212.6/icr/index.html

INCLUSive - (Found July 2, 2008 )

INCLUSive is a set of tools for the analysis of gene expression data and the discovery of cis-regulatory sequence elements.
http://www.esat.kuleuven.ac.be/inclusive

JASPAR - (Found July 2, 2008 )

JASPAR is a non-redundant, curated collection of transcription factor binding profiles. Each profile is generated from published, experimentally defined eukaryotic transcription factor binding sites.
http://jaspar.cgb.ki.se/cgi-bin/jaspar_db.pl

jPREdictor - (Found July 2, 2008 )

jPREdictor predicts cis-regulatory elements using short motifs that are known to bind regulatory proteins. Predictions are made by searching for clusters of these motifs, and weighting these clusters by applying a positive or negative training sets to score the sequence.
http://bibiserv.techfak.uni-bielefeld.de/jpredictor/

ARGO - July 2, 2008

ARGO is a tool for the detection and visualization of sets of region-specific degenerate oligonucleotide motifs in the regulatory regions of eukaryotic genes.
http://wwwmgs.bionet.nsc.ru/mgs/programs/argo/

ACMES - (Found July 2, 2008 )

ACMES (Advanced Content Matching Engine for Sequences) is a server that can be used to search for short repeats (between 3 and 10 000 bases) across multiple species. Users can limit results of a search by keyword searches.
http://acmes.rnet.missouri.edu/