ConSite - Transcription factor binding site detection using phylogenetic footprinting
The Gene Characterization Index - a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described
JASPAR - Transcription Factor Binding Profile Database
MeSHOP - Using Medical Subject Heading Overrepresentation Profiles (MeSHOPs), an entity of interest can be robustly summarized, quantitatively identifying associated biomedical terms and suggesting indirect associations
MSCAN - Algorithm that detects clusters of transcription factor binding sites in genomic sequences
NHRscan - A computational predictor of nuclear hormone receptor binding sites
oPOSSUM v3 (2012) A web-based system for the detection of over-represented conserved transcription factor binding sites and binding site combinations in sets of genes or sequences. For the previous version of oPOSSUM see v2 (2008) below.
ORCA - Transcription factor binding site detection using phylogenetic footprinting (alternative to ConSite)
PAZAR - An open-access system for the collection and dissemination of regulatory sequence annotation
Phylofoot - Tools for phylogenetic footprinting
TFBS - Perl modules for transcription factor binding site detection and analysis
TFCat - TFCat is a catalog of mouse and human TFs based on a reliable core collection of annotations obtained by expert review of the scientific literature.
TFe - An online encyclopedic collection of well-studied transcription factor proteins in the human, mouse, and rat genomes
Retired Software Tools
GeneLynx - A portal to the human genome. This tool was developed to fulfill a need for easily accessible gene information at a particular point in time. Having fulfilled its purpose, this tool has been retired. Current tools are available to provide similar services.
Gene Set Builder - A tool for collation, curation and distribution of sets of genes
GOToolBox - Functional Investigation of Gene Datasets
dbMTN - Multiple Tissue Northern Blot Comparison Tool
NovelFam3000 - A bioinformatics tool created to accelerate characterization of gene families sharing uncharacterized protein domains
oPOSSUM v2 (2008) - Web-based analysis of over-represented transcription factor binding sites
OrthoSeq - Alignment of DNA sequences
RAVEN - Regulatory analysis of Variation in ENhancers
SAGE2Splice - A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome
Ulysses - Protein Interactions Conserved Across Evolution