Query on MEME sites

[Arun Prasanna]

Hi,

In the MEME html output, Sites says that "The number of sites contributing to the construction of the motif."  I used nmotifs = 50 and for few motifs, sites showed a value of 2 and the maximum for few motifs were 14. My search set had a total of 63 sequences. Since, MEME searches for short subpatterns in whole dataset the site should be of greater value right, if not it is present in all 63 ? Does it mean that, I need to run a randomly generated control sequence set of same size & length to validate my results ?

Thanks in Advance,

AP

[CharlesEGrant]

MEME is also a greedy algorithm, so as soon as it has enough information to estimate the statistical significance of a motif, it reports that motif and begins looking for other motifs. The MEME web applications defaults to requiring a minimum of 2 sites for a motif. You can adjust the minimum and maximum number of sites required under the "Advanced Options" section of the web page, or with the -minsites and -maxsites options for the command line version of MEME.