What is this?
Links to other programs.
Deal with conserved motifs in two or more aligned sequences:
BindGene - Search for conserved motifs defined by weight matrices in two or more aligned sequences or in a single sequence.
ConSite - Search for conserved TFBS in two aligned/two homologous or a single sequence.
Footer - Searches for user defined motifs in aligned human and rodent sequences.
MULTIPIPMAKER tools - 'Multi_pat' searches for a user specified nucleotide pattern and 'Tffind' identifies matches to weight matrices.
MultiTF - Identifies matches to TRANSFAC weight matrices in MULAN or GALA aligned sequences.
Sockeye - Identifies matches to weight matrices (including TRANSFAC and JASPAR) in aligned sequences.
RVISTA - Identifies matches to TRANSFAC weight matrices and IUPAC strings
in user supplied aligned sequences.
Deals with unaligned sequences:
AliBaba2 - Search using TRANSFAC matrices.
BEARR - Search for matches to IUPAC consensus strings or weight matrices in the promoter regions of co-expressed/co-regulated genes of interest.
CompareProspector - Searches for over-represent patterns in sequences, using Gibbs sampling, that are conserved across species. 20-40 input sequences are recommended.
CONREAL - Identifies conserved motifs (represented by weight-matrices) in user supplied sequences or from sequences obtained via the tool. The tool uses multiple alignment programs and weight-matrix databases.
CONSEQ - Takes a list of co-expressed/co-regulated genes and identifies human/mouse orthologues. Conserved regions are then scanned for matches to TRANSFAC matrices.
FootPrinter - Searches for user defined motifs in a set of unaligned but homologous sequences.
MATCH - Search using TRANSFAC matrices (requires registration for free academic access).
MatInspector (Professional) - Search using TRANSFAC matrices and IUPAC strings (requires registration for free academic access - limited uses/month).
MotifScanner - Search sequence using TRANSFAC matrices. Considers background noise of sequence.
MSCAN - Search using user defined or JASPAR2 matrices.
PROMO v3 - Search using TRANSFAC matrices.
P-MATCH - Search using TRANSFAC matrices and pattern matching (requires registration for free academic access).
TESS - Search using IUPAC strings or weight matrices.
TFM-Explorer - Takes a list of co-expressed/co-regulated genes and searches for locally over-represented TFBSs. Takes advantage of spatial conservation in the sequence and supports multiple species (human/mouse/rat).
TOUCAN2 - A workbench for regulatory sequence analysis on metazoan genomes: comparative genomics, detection of significant transcription factor binding sites, and detection of cis-regulatory modules (combinations of binding sites) in sets of coexpressed/coregulated genes.