Does anyone have any recommendations for motif-finding algorithms that can use ChIP-seq scale data? Approaches that can use all of the data, ideally incorporating ranking information, rather than just running MEME or similar on the top 50 ChIPseq peaks.
I'm also looking for methods that can handle motifs with substructure - for example I'm looking at some TFBS data and the binding site has left and right half sites which can appear on their own, or together in different orientations and with different spacers between them. Any suggestions on strategies for de novo identification of such patterns?
I've also seen a program called HMS (http://www.sph.umich.edu/csg/qin/HMS/) meant for ChIP-seq motif finding, but I haven't tried it yet. There is at least one more out there.
Awesome. Thanks Mikael :)