ConSite - Transcription factor binding site detection using phylogenetic footprinting
dbMTN - Multiple Tissue Northern Blot Comparison Tool
Gene Set Builder - A tool for collation, curation and distribution of sets of genes
The Gene Characterization Index - a bioinformatics method for scoring the extent to which a protein-encoding gene is functionally described
GOToolBox - Functional Investigation of Gene Datasets
JASPAR - Transcription Factor Binding Profile Database
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) WARNING this is a beta test version and is still under development. Please use with caution. For the previous stable version of oPOSSUM use v2 (2008) below.
oPOSSUM v2 (2008) - Web-based analysis of over-represented ranscription factor binding sites
ORCA - Transcription factor binding site detection using phylogenetic footprinting (alternative to ConSite)
OrthoSeq - Alignment of DNA sequences
PAZAR - An open-access system for the collection and dissemination of regulatory sequence annotation
Phylofoot - Tools for phylogenetic footprinting
RAVEN - Regulatory analysis of Variation in ENhancers
SAGE2Splice - A tool that uses unmapped SAGE tags to predict novel splice junctions in the genome
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
Ulysses - Protein Interactions Conserved Across Evolution
Project Websites
Pleiades Promoter Project: Genomic Resources Advancing Therapies for Brain Disorders
Expression platform comparison
Ulysses project details
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.
NovelFam3000 - A bioinformatics tool created to accelerate characterization of gene families sharing uncharacterized protein domains


