Questions on MEME 4.11.2 -maxsites

[Jaime Alvarez Benayas]

Hello,

I am performing a run with around 1000 DNA sequences ranging from 400-2400bp each. I run MEME with the following parameters:

meme meme.fasta -dna -revcomp     -mod anr     -nmotifs 40     -oc ./ctmpmTK7Vv     -maxsize 300000               -minw 5 -maxw 30

The log of the execution proceeds as follows:

Initializing the motif probability tables for 2 to 50 sites...
nsites = 50
Done initializing.
SEEDS: highwater mark: seq 502 pos 800


seqs=   503, min= 400, max= 2400, total=   299200


motif=1
SEED WIDTHS: 5 7 9 12 16 22 30

Due to the limit (-maxsize 300000) the 1000 sequences have been trimmed to 503. However, I don't understand why maxsites=50 by default. According to the MEME documentation (http://meme-suite.org/doc/meme.html?man_type=web):

-maxsites n When the motif site distribution model allows, MEME will attempt to find motifs with at most n sites. When the distribution model is OOPS this is ignored and the number of sites is set to the number of sequences. When the site distribution model is ZOOPS this is set to the number of sequences, however when it is ANR this is set to min(5 × sequence count, 600).

According to this, shouldn't maxsites be min(5x503, 600) = 600?

Also, in the run with maxsites=50, what happens with motifs which have more than 50 site coincidences? Are they still reported?

Thanks!

[CharlesEGrant]

Hi Jaime,

This is due to a longstanding bug in MEME. The default value of maxnsites for the ANR/TCM model had a maximum of 50, not 600 as specified in the documentation. This will be fixed in the next release of the MEME Suite, probably in the next couple of weeks. In the mean time you can override the default by setting the '-maxsites' option.

Also, in the run with maxsites=50, what happens with motifs which have more than 50 site coincidences? Are they still reported?

The maxsites parameter determines the maximum number of putative motif sites that will be used as evidence for the motif. If the number of sites for a motif exceeds the maximum, some of those sites will simply be ignored, but the resulting motif will still be reported.