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Best Tools For Motif Finding And/Or De Novo Motif Discovery?

Hi everybody,

I'm looking for tools to do motif finding and/or de novo motif discovery on large genomic datasets (ChIP-on-ChIP, ChIP-Seq, DamID).

What are your suggestions, Biostar?

Thanks!

chip-seq motif genomics
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updated by sascha-ott • sascha-ott • written by enricoferrero enricoferrero

6 answers

How about GimmeMotifs, i have even written a brief review on BioStar :)

http://www.biostars.org/post/show/45166/gimmemotifs-motif-discovery-by-consensus/

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written by Ian Ian

I found meme suite really useful.

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written by Leszek Leszek

Hi, I would also add MotifViz.

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written by Anima Mundi Anima Mundi

Another vote for MEME. I've never used it for ChIP-Seq but it works very well with proteins. The website is nice, but the command line application is much more powerful.

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written by Vitis Vitis

GimmeMotifs and completemotifs. :)

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written by Dataminer Dataminer

When you have to do motif finding for a large number of gene clusters it can be a challenge processing all of the results one-by-one. We had this problem in our work and came up with this tool which runs MEME for a number of clusters in parallel and provides a single, interactive output page:

Tool:
http://wsbc.warwick.ac.uk/wsbcToolsWebpage/

Paper:
http://bioinformatics.oxfordjournals.../1696.abstract

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written by sascha-ott • sascha-ott

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