Retaining all contributing sites from command line run of MEME

[Angus Hilts]

Hi everyone,

I am interested in looking at the specific instances of motifs after running MEME. The issue is that in some of my data sets, I have a large number of sites, which MEME seems to suppress. Is there a way to increase the number of sites that MEME will report so that I don't keep hitting the limit and can then extract the sequences themselves afterwards?

thanks in advance!

[cegrant]

Have you looked at the -nsites -minsites, and -maxsites options described in the MEME documentation? Note that depending on your choice for the site distribution (the -mod option model one or all of these parameters may be ignored. If you choose the "only one per sequence" (OOPS)  model you are telling MEME that each sequence contains exactly one site, so the number of sites used is always equal to the number of sequences. If you choose  the "zero or one per sequence" (ZOOPS) model you are telling MEME that each sequences contains at most one site, so the max sites parameter will always be equal to the number of sequences. If you choose the "any number of repetitions" (ANR) model the maximum number of sites that can be used is set to 5 times the number of sequences.

Typically you'd just let MEME use the default number of sites for the model you select, and then use the discovered motifs to scan for other sites matching the motif with FIMO. You'd usually only adjust the number of sites to be used if the motifs discovered had low statistical significance and you wanted MEME to try a bit harder to find supporting evidence.

Depending on  your needs you may want to switch to STREME for motif discovery: it's faster and more thorough.