Motif discovery

[Ayyappa_kumar]

I have performed the motif detection using MEME, it resulted me with the motif of 50 bp now and later I have performed the motif search using the TOM TOM and I have got some three known motifs with 30 bp each. Now i am confused with the obtained motifs, is it common to get motifs with 50 bps? Any suggestions will be appreciated

[GenoMax]

Quote from MEME Site:

MEME will analyze your sequences for similarities among them and produce a description (motif) for each pattern it discovers

MEME is going to find patterns within the limits you specify (defaults for web MEME are: Longer than 3 but shorter than 50). It will start looking for the longest patterns it can find. If you want to look for motifs that are shorter then adjust these parameters when you run MEME.

TomTom is comparing your motif against known motifs database so even though a 50 bp pattern was identified in your sequences only 30bp match a known motif (I assume that is what you mean in your post).

[SNPsaurus]

I recently used RSAT (http://rsat.ulb.ac.be/peak-motifs_form.cgi) for motif discovery with a method related to ChIP-Seq assaying functional enhancer strength on a genome-wide basis. RSAT produced a nicer output in my opinion, and it came up with the canonical motif for several of the transcription factors known to be involved in the cellular response.