TFBScluster - Genome-wide.
Links to other programs.
TFBScluster flanking sequence can be used in the design of transfection experiments:
Primer3 can be used to create primers to PCR a region from the flanking sequence.
NEBcutter can be used to check that vector restriction
sites are not present in the proposed PCR fragment.
Other similar web tools:
SynoR - Search for clusters of TRANSFAC motifs with user specified spatial configurations. The relationship to UCSC known genes to the candidate clusters is presented. An analysis of the GO terms representing the genes can also be performed.
- Find clusters of JASPAR defined TFBSs found in orthologous sequences.
Custom species comparisons can created with their stand-alone tool.
Co-expressed gene data
Bioprospector - Search for clusters of over-represented motifs in the promoter regions of co-expressed/co-regulated genes of interest.
CREME - Search for clusters of weight matrix defined TFBS in the promoter regions of co-expressed/ co-regulated genes of interest.
ModuleSearcher and ModuleScanner - Search for clusters of TRANSFAC weight matrixes and scan the genome for predicted clusters.
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
Single/aligned user sequences
[PC program] CATS - Search for clusters of IUPAC consensus strings in a single sequence.
Cister - Search for predefined motifs in a single sequence.
Cluster-Buster - Search for clusters of weight matrix predefined TFBS in a single sequence.
ConSite - Search for clusters of TRANSFAC weight matrixes that are conserved between two user supplied sequences.
Enhancer - Search for clusters of IUPAC consensus sequences in worm and plant genomes.
MSCAN - Search for clusters of TRANSFAC weight matrixes and in selected unaligned sequences.
rVISTA - Identifies matches to TRANSFAC weight matrices in user supplied aligned sequences, also allows clustering of TFBS.
zPicture - Visualise a pairwise alignment and identify clusters of
selected TRANSFAC weight matrices or IUPAC consensus sequences.
AHAB - Search for user defined or pre-defined motif matrices in a single user supplied sequence, in a single fly genome, or in the regions of Drosophila melanogaster that are conserved in the Drosphila pseudoobscura genome.
cis-analyst - Search for user defined motifs in the Drosophila melanogaster that are conserved with the Drosphila pseudoobscura genome.
Fly Enhancer - Search for clusters of IUPAC consensus strings in the Drosophila melanogaster genome.
Target Explorer - Search for clusters of weight matrix defined TFBS in Drosophila genomes.