Hi all I have 2 kb long sequence which is promoter region of a gene. From that sequence I would like to pinpoint transcription factor binding sites of smad3. How can I do that and is it possible with JASPAR?
JASPAR allows exporting motifs in MEME format which you can use along with FIMO from the MEME suite to look for specific motif occurrences in your sequence(s). As opposed to exact string matching it takes into consideration the probability of each base occurring per-position since chromatin binding proteins can be promiscuous with their binding sites.