Hi,

I have a question in this regard. I ran MEME on a set of 100 co-regulated genes expecting the presence of a few or more common TFBS. The command I used was: ./meme coreg_promoters.fasta -dna -mod zoops -minw 6 -maxw 14 -nmotifs 10 -maxsize 65000

I did get 10 motifs found on my sequence set, but all of them were semi-transparent, implying e-value greater than 0.05. Next, I went on to check with

./meme coreg_promoters.fasta -dna -mod zoops -minw 6 -maxw 14 -nmotifs 10 -maxsize 65000 -evt 0.05

As expected, the output said "No significant motifs found !'

Should I consider those semi-transparent motifs or discard them ? How can one decide in this case ?

Thanks,

AP