-evt argument in meme not working.

[Trevor C]

Hello, 

In the MEME program I am trying to get the function to return all motifs that are calculated to have a smaller E-value than some threshold ev (say ev = 0.5).

I have deliberately created a fake data set of primary sequences which have more than motif inserted (I inserted 4). When i use the -evt option, MEME returns only 1 motif with the line:
"Stopped because requested number of motifs (1) found." This is, I believe, contradictory to what -evt says it does: "MEME will stop searching for motifs if the last motif found has an E-value > ev."

When I use the -nmotifs option all of my 4 motifs are returned with E-value lower than threshold. Therefore I am inclined to believe that the -evt option is not working properly. That or I am misunderstanding something.  

My command line is :

meme <primary sequences> -oc <output> -dna -mod anr -evt 0.5

Any thoughts? 

Best wishes, 

Trevor

[cegrant]

The problem is that MEME is a greedy algorithm and is not guaranteed to identify motifs in strictly increasing order of E-value. The heuristics MEME uses are good enough that statistically significant motifs will tend to be found first, but it isn't a guarantee. For that reason we don't recommend using the -evt option. It's just not very useful, since it can cause you to miss significant motifs if MEME happens to find a motif above the threshold first.