5.7 years ago by
Duarte, CA
In general, there are databases like TRANSFAC and JASPAR for transcription factor binding motifs, and various tools that utilize the matrices present in those databases.
I think this interface provides the functionaity that you are looking for:
http://rulai.cshl.edu/cgi-bin/TRED/tred.cgi?process=searchTFGeneForm
More commonly, I tend to work with lists of differentially expressed genes, and I am looking for what motifs are enriched in a given gene list. GATHER is one good, open-source tool for doing this (although there certainly are others):
http://gather.genome.duke.edu/
If you are interested in de novo prediction of enriched motifs, I would recommend SCOPE:
http://genie.dartmouth.edu/scope/