BiasAway - An open-access tool for generating multiple different sequence backgrounds of comparable nucleotide composition relative to a set of input sequences
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.
ORCAtk - 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_Visualization - An open-access tool for visualizing and assessing transcription factor topological motif enrichment in ChIP-Seq datasets
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
TFFM - Transcription Factor Flexible Models (TFFMs) are hidden Markov model (HMM) representations of TFBS motifs. This online tool allows you to generate TFFMs and scan sequences with them.
Retired Software Tools
Expression platform comparison
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