Finding overrepresented sequence motifs in a set of transcripts

Question

[Paul]

Hello,

I have a list of miRNAs that I belive to be co-regulated post-transcriptionally. I would like to query the sequence of the mature miRNAs for over-represented sequence motifs. Does anybody have any idea if there is an exsiting tool that could be easily adapted to solve this problem?

Thanks!

Answer 1

[pld]

You could check out MEME, but I've only used that for longer bacterial promoters, but the principle is the same. Or even run something more basic like generating a sequence logo using WebLogo. A sequence logo will give you the degree of conservation at each position as well as the frequency of bases at those positions.