Discovered motif from MEME shows no enrichment in SEA

[Samuel Chen]

Hi MEME Suite team, 

I have been using the discriminative mode of MEME to discover motifs that are enriched in my primary sequence set relative to the control set (using zoops as site distribution, and 0-order as background model). 

In many of the cases, MEME returned significant motifs with very low E-values.

However, when I took the discovered motifs from MEME and ran them across SEA (using the same primary and control sequence sets as I did with MEME, and all other parameters as default), most of the motifs turned out to be not significantly enriched. 

Is this something I should be expecting? Or are there some parameters I set incorrectly?

Thank you.

Best,

Samuel

[cegrant]

That is a little disconcerting but I'd need to see the inputs and results to debug the problem. You might consider using STREME rather than MEME. STREME is a newer de novo motif discovery program and uses the same objective function as SEA. If you still have concerns it would be helpful if you could forward us copies of your MEME/STREME, and SEA output, and perhaps your input files as well. That would let us troubleshoot any problems.