I have a set of sequences for which I have identified a list of significant motifs through MEME.
I then used FIMO to find specific regions in my sequences where the identified significant motifs were enriched. It gives me enriched locations for my motifs. It does not give me a list of known TFs.
In parallel, I used TomTom to align my significant motifs with known TF motifs. It gives me a list of known TFs with p-values that were not encouraging. But, it does not provide me with the list of enriched locations in which the known TFs were found.
CentriMo provides me with a list of how the known TF motifs (different and larger than those provided by TomTom) are distributed within my sequences and the list of matching sequences too. However, I am unable to export this list of matching sequences for all the TFs.
My question is, is there a way to export this list of matching sequences? It would be a huge exercise if I have to take them from the web result for each of the TFs that I require.
Basically, my input is a list of my motifs, my sequences, AND the TF database from which known TF matches should be displayed as enriched. And as output, I wish to have locations of my sequences where my motifs are enriched, and the matching known TF motif.
I hope I have been clear!