Hello guys!
I’m looking for a software that can find unknown consensus sequences between some promoters regulated from the same transcriptional factor. I’ll try to explain my problem in details: We are studying a transcriptional factor and we know that the deletion of this gene causes the deregulation of some other genes. We think that this transcriptional factor binds a common consensus sequence on the promoters of the deregulated genes but we don’t know anything about this consesus. We just know that, probably, there is a common consensus sequence in these promoters. Now what we want to do is to allineate our promoters sequences to find some short (6-12 bp) common sequences that could be the transcriptional factor consensus.
Thanks in advance!
You could try a motif-finding strategy (see this paper) however, promoter regions usually share more than one transcription factor and different transcription factors can bind similar sites. I think the best approach here would be experimental (see this paper for ideas).
You can also have a look at known TF binding sites in public databases such as in GTRD.