Bioinformatics Links Directory : Gene Regulation

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

PromH - (Found July 2, 2008 )

PromH predicts transcription start sites (TSS), TATA boxes, and transcription factor binding sites (TFBS) in promoter regions using pairs of orthologous sequences.
http://www.softberry.com/berry.phtml?topic=promhg&group=programs&subgroup=promoter

PromAn - (Found July 2, 2008 )

PromAn is an integrated promoter analysis platform that takes a genomic sequence of interest and considers information on orthologous genomic sequence(s), user submitted patterns, and public databases to predict transcription start sites (TSS), transcription factor binding sites (TFBS), and to carry out phylogenetic footprinting.
http://bips.u-strasbg.fr/PromAn/

oPOSSUM - (Found July 2, 2008 )

oPOSSUM is a web-based system for the detection of over-represented transcription factor binding sites in the promoters of sets of genes.
http://www.cisreg.ca/oPOSSUM_new/

P-Match - (Found July 2, 2008 )

P-Match is a transcription factor binding site identification tool that increases its accuracy by combining weight matrix and pattern matching approaches. Registration at the site is free and is required to use P-Match.
http://www.gene-regulation.com/cgi-bin/pub/programs/pmatch/bin/p-match.cgi

PAP - (Found July 2, 2008 )

Promoter Analysis Pipeline (PAP) can identify potential transcriptional regulators for sets of co-expressed genes and identify potential regulatory targets of transcription factors.
http://appserver.wustl.edu:8080/webtools_v4_2/PromoterSearch.do

PHIRE - (Found July 2, 2008 )

Phage In silico Regulatory Elements (PHIRE) is a standalone program in Visual Basic which performs a string-based search on bacteriophage genome sequences discovering and extracting blocks displaying sequence similarity corresponding to conserved regulatory elements contained within these genomes.
http://www.biw.kuleuven.be/logt/PHIRE.htm

PlantTFDB - (Found July 2, 2008 )

Plant Transcription Factor Database (PlantTFDB) is database that attempts to identify a comprehensive set of plant genes coding for transcription factors. A web interface to the database allows users to browse by species, search using a sequence identifier, or query using BLAST.
http://plntfdb.bio.uni-potsdam.de/v1.0/

POBO - (Found July 2, 2008 )

A server for the detection, comparison and verification of transcription factor binding site motifs in promoters. POBO bootstrap analysis applied to one or two clusters of co-regulated genes detects motifs under extreme levels of representation.
http://ekhidna.biocenter.helsinki.fi/pobo

POCO - (Found July 2, 2008 )

POCO searches a set of promoters from co-expressed genes for nucleotide patterns that are over-represented.
http://ekhidna.biocenter.helsinki.fi/poco/

POXO - (Found July 2, 2008 )

POXO is a series of tools that can be used to discover, search, and verify transcription factor binding sites (TFBS) from sets of co-expressed genes.
http://www.bioinfo.biocenter.helsinki.fi/poxo