Hi, I don't have much experience with motif searches, and I would like to hear your advice on the following task:
I have a DNA sequence (~300 bp) which hypothetically contains a regulatory motif. For example, a 300 bp region upstream the TSS of a gene. There is no prior knowledge of what could be binding there, and I want to have some predictions. What tool would be best to scan for motifs similar to any of the known TF binding motifs in Drosophila? Further, what could be a good tool to submit an alignment from multiple species, and find a conserved motif? (again Drosophila; I don't want to find any motif, but a motif corresponding to a known factor).
Thanks in advance