Recommendations for a good motif-finder, for short K-mers?
Hi, I am trying to find a motif in a few thousand 100bp long sequences, and I think the motif I am trying to find is very short (a few bp, perhaps even 3-4bp long) I tried MEME and HOMER, but didn't find any significant motifs. Any recommendations?
1 answer
Log in to answer this question.
More posts like this
-
Identify binding motifs within large super enhancer region
written by mkunika •
-
Help with HOMER motif profile plots
written by venu
-
Can you get mpileup to report positions with coverage of 0?
written by blur
-
Aligning to ultra-short reference sequence
written by spaladug •
-
HOMER find motifs for each sequence
written by bsharmi6 •
-
meme-suite: How does FIMO works?
written by GR
-
Motif prediction with MEME
written by arunprasanna83 •
-
Using Homer Programs For Denovo Motif : Different Results Among Its Own Versions
written by RT •
-
Parameters That Determine Meme Speed And Homer Speed For Motif Discovery?
written by user
-
Dna Motif Discovery
written by k.nirmalraman
Significant in which sense? Compared to another set of sequences? Compared to some background model? Do you expect the motif to occur multiple times in each sequence or just once? Would you expect the motif to be evolutionarily conserved?
whatever way I tried, I seem to be at a loss - HOMER I tired with background datasets, with different datasets... nothing. I get very few possible motif option with p-values that are just not reliable... I thought perhaps a short motif was too short for these algorithms? As for the motif itself, I have a suspicion it would be something like GC-rich, 4bp sequence, as similar analyses to what I do seem to end up like that, but I don't know if I am correct... Any insight would be greatly appreciated