The minsites option does not work?

[Joel Wallenius]

Hello!

When I try:


... -minsites 414 -maxsites 1242 ...

It still says "Initializing the motif probability tables for 2 to 1242 sites..."


What gives? Why can't I tell it to expect the motif to appear with an overall frequency of between 0.3 and 1?



Thanks!

[CharlesEGrant]

The minsites and maxsites options are described here:

http://meme-suite.org/doc/meme.html

I think you’ve misunderstood their purpose.

MEME makes an initial guess at likely motif sites and the motif PWM. It then iteratively adjusts the candidate sites and PWM to increase the statistical significance of the discovered motif.

   

minisites sets the minimum number of candidate motif sites that must be found before MEME will accept a candidate motif as a reportable motif.

maxsites sets the maximum number of candidate motif sites that will be considered in evaluating a candidate motif.

Setting the MEME model parameter to oops (Only one motif per sequences) overrides the minsites and maxsites parameters since it specifies that each sequence contains exactly one instance of a motif.

[Joel Wallenius]

Hello Charles!

Yes I very much misunderstood their purpose. I suppose I should have read a beginner's guide on motif finding before I tried to interpret the MEME help section.

So if I have 1000 sequences, and put -minsites 500, using zoops (it is the default I think?), that means MEME will only report motifs that were found in at least 500 positions among the 1000 sequences?

[CharlesEGrant]

Right, and for the ZOOPS model that means that at least 500 sequences have to contain an instance of the motif.

[Joel Wallenius]

Thank you Charles!