MEME parameters

[gene_x]

Have anyone here used MEME tools? Specifically with de novo motif discovery using meme

Can you share your experience on choosing the parameters, like motif width etc? and on how to run things at a relatively fast speed?

Thanks.

[john_nl]

I would perform runs with width ranging from from 6-8, 8-10 and 10-12. This is because MEME "likes" to discover the longest motif it can in my experience. Zoops mode is probably most sensible but also try 'any number of repetitions'.

[gene_x]

good suggestion.. i first tried minimum with 6 and maximum width 50 and it takes a really long time and the result of are basically repeats, not motifs..