Using MEME-suite to find sigma-factor binding sites (or other broad motifs)

Question

[predeus]

Hello all,

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.

Answer 1

[Asaf]

When I was a bioinformatics TA we taught MEME and I was trying to come up with an example that will work, it was really hard. The example we used eventually was Spo0A from Bacillus. The RpoD Motif is hard to find using MEME, a probabilistic graphic model that will include the space between the -35 and -10

[predeus]

Thank you. Do you know what is the best TF motif database for bacteria?