Question

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

2

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12.4 years ago

enricoferrero ▴ 910

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 • 8.8k views

ADD COMMENT • link updated 10.1 years ago by sascha-ott ▴ 10 • written 12.4 years ago by enricoferrero ▴ 910

score 2 · Answer 1 · 2012-07-20

2

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12.4 years ago

Ian 6.1k

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

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

ADD COMMENT • link 12.4 years ago by Ian 6.1k

score 1 · Answer 2 · 2012-07-20

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12.4 years ago

Leszek 4.2k

I found meme suite really useful.

ADD COMMENT • link 12.4 years ago by Leszek 4.2k

score 1 · Answer 3 · 2012-07-20

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12.4 years ago

Anima Mundi ★ 2.9k

Hi, I would also add MotifViz.

ADD COMMENT • link 12.4 years ago by Anima Mundi ★ 2.9k

score 1 · Answer 4 · 2012-07-26

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12.3 years ago

Vitis ★ 2.6k

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.

ADD COMMENT • link 12.3 years ago by Vitis ★ 2.6k

score 1 · Answer 5 · 2012-07-30

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12.3 years ago

Dataminer ★ 2.8k

GimmeMotifs and completemotifs. :)

ADD COMMENT • link 12.3 years ago by Dataminer ★ 2.8k

score 1 · Answer 6 · 2014-10-17

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