Significant Differences Of Motif Enrichment Between Two Different Groups Of Sequences

Question

[Geparada]

Hi!

I have a database of hexamers and decamers that are involved in splicing regulation. I want to see if there are any difference in the content of this sequences between two types of splice junctions.

Do you any tool that could help me to do this?

Thanks for your time!!!

Answer 1

[Asaf]

You can try discriminative MEME

[Geparada]

I don't want to find motifs de novo, I just want to look for motifs that are in my database... but I'll try your approach, thanks.

Answer 2

[Anthony Mathelier]

You can look at the number of sites in each one of your data sets and then compute a Fisher-score and a Z-score similarly as oPOSSUM does for TFBSs.

oPOSSUM paper: http://www.ncbi.nlm.nih.gov/pubmed/?term=22973536

Answer 3

[tarajano]

I'm not totally sure if it could help you but, have you heard about SLiMFinder? SLiMFinder: a web server to find novel, significantly over-represented, short protein motifs http://nar.oxfordjournals.org/content/early/2010/05/23/nar.gkq440.full

Answer 4

[cherdt]

The FIMO tool (part of MEME Suite) will search a given sequence for a set of given motifs: http://meme.nbcr.net/meme/fimo-intro.html