I have figured out how to extract fasta sequences from a bed file and then run motif discovery on it. Similarly, I have run my motif results in TOMTOM to identify proteins with similar motifs. But, I have yet to find a reliable way of searching for known DNA motifs by protein ID/name. What I want, ideally, is to input a TF protein name and get a list of known DNA motif associated with said TF. Any suggestions or recommendations on how to do this would be greatly appreciated. I figure MEMEsuite has a way but it is not outwardly clear. Cheers
I have a few answers on Biostars and Bioinformatics Stack Exchange about using FIMO.
Here's a starter: A: TF binding site analysis - how to filter hits?
The idea is that you generate a whole-genome set of TF binding sites for your TF database of interest, and then you filter them as needed for your regions of interest, if needed.