Bioinformatics Links Directory : Gene Regulation

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

SSA - (Found July 2, 2008 )

Signal Search Analysis (SSA) allows for the analysis of nucleic acid sequence motifs that are positionally correlated with a functional site (e.g. a transcription start site).
http://www.isrec.isb-sib.ch/ssa/

STAMP - (Found July 2, 2008 )

STAMP is a tool for exploring DNA-binding motif similarities by providing resources for motif alignment, similarity and database matching.
http://www.benoslab.pitt.edu/stamp/

Stubb - (Found July 2, 2008 )

Stubb uses a probabilistic model and a maximum likelihood approach to detect clusters of transcription factor binding sites (TFBS) in genomic sequences (limit of 100 Kb). It can also use related genomes to improve module prediction accuracy.
http://stubb.rockefeller.edu/

Zinc Finger Tools - (Found July 2, 2008 )

Zinc Finger Tools provides several tools for selecting zinc finger protein target sites and for designing the proteins that will target them.
http://www.scripps.edu/mb/barbas/zfdesign/zfdesignhome.php

Footer - (Found July 2, 2008 )

Footer is a tool for identifying highly-probable binding sites of known transcription factors using phylogenetic footprinting principles to analyse two homologous DNA sequences.
http://biodev.hgen.pitt.edu/Footer/

Consite - (Found July 2, 2008 )

Detect transcription factor binding sites in genomic sequences using phylogenetic footprinting and experimentally-confirmed binding profiles.
http://www.phylofoot.org/consite/

CRSD - (Found July 2, 2008 )

Composite Regulatory Signature Database (CRSD) is a microarray analysis pipeline aimed at the discovery of motifs involved in gene regulation including microRNA signatures and transcription factor binding sites (TFBS).
http://140.120.213.10:8080/crsd/main/home.jsp

DAVID Bioinformatics Resources - (Found July 2, 2008 )

The Database for Annotation, Visualization and Integrated Discovery (DAVID) provides a comprehensive set of functional annotation tools for investigators to understand biological meaning behind large list of genes.
http://david.abcc.ncifcrf.gov/home.jsp

Defining Transcriptional Programs in Vascular Endothelium - (Found July 2, 2008 )

This website contains microarray analysis software (Argus and Z-pool), an Endothelial Cell Expression Database, and other resources related to Vascular Endothelium research. See the PubMed abstracts for more information.
http://www.vessels.bwh.harvard.edu/

DEREF - (Found July 2, 2008 )

Dragon Estrogen Response Element Finder (DEREF) allows the discovery of transcription factor binding sites (TFBS) in vertebrate genomic sequences.
http://sdmc.lit.org.sg/ERE-V2/index