I've used MEME suite (meme-chip) before to identify motifs in ChIP-seq data and it worked OK the few times I've used it.
However, right now I'm trying to identify binding sites of several bacterial sigma factors (including core rpoD), and it's not doing a very good job at all. Part of the problem might be that it's an asymmetrical motif with a variable distance between -10 and -35 sub-motifs.
At any rate, what is a good approach here? Thank you for any suggestions, as always.