4.5 years ago by
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:
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):
If you are interested in de novo prediction of enriched motifs, I would recommend SCOPE: