Finding overrepresented sequence motifs in a set of transcripts
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8.3 years ago
Paul ▴ 760

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!

mirna sequence • 1.7k views
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8.3 years ago
pld 5.0k

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.

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