Hi I am wondering whether there are any good approaches for creating a census motif from a number of TFs in the same family, that are very closely related. For instance from Hox TFs or ZNFs, so if you have PWMs for individual members what is the best way to go about creating a consensus sequence? Thanks!
I've also used PWMclus in "CCAT: Combinatorial Code Analysis Tool for transcriptional regulation." for a task like this with good results. I will warn that this type of analysis wouldn't work well for many families (especially Zinc Fingers) with very diverse motifs if you choose a single consensus motif. You have to choose 1 consensus per cluster.