Question

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

2

Entering edit mode

11.8 years ago

enricoferrero ▴ 900

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 • 8.5k views

ADD COMMENT • link updated 9.5 years ago by sascha-ott ▴ 10 • written 11.8 years ago by enricoferrero ▴ 900

score 2 · Answer 1 · 2012-07-20

2

Entering edit mode

11.8 years ago

Ian 6.0k

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 11.8 years ago by Ian 6.0k

score 1 · Answer 2 · 2012-07-20

1

Entering edit mode

11.8 years ago

Leszek 4.2k

I found meme suite really useful.

ADD COMMENT • link 11.8 years ago by Leszek 4.2k

score 1 · Answer 3 · 2012-07-20

1

Entering edit mode

11.8 years ago

Anima Mundi ★ 2.9k

Hi, I would also add MotifViz.

ADD COMMENT • link 11.8 years ago by Anima Mundi ★ 2.9k

score 1 · Answer 4 · 2012-07-26

1

Entering edit mode

11.8 years ago

Vitis ★ 2.5k

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 11.8 years ago by Vitis ★ 2.5k

score 1 · Answer 5 · 2012-07-30

1

Entering edit mode

11.7 years ago

Dataminer ★ 2.8k

GimmeMotifs and completemotifs. :)

ADD COMMENT • link 11.7 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