Question

How Can I Find Specific Motifs Of Promoter Sequences Of A Large Number Of Genes

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11.3 years ago

sanchezcavani ▴ 220

I want to find some upstream regulatory motifs shared commonly in my genes. The case is that the upstream regions of my genes do not often show a high global sequence similarity thus an alignment of all of the sequences is not easy to do. Does anyone have any idea about how to do it? Thanks a lot!

promoter motif • 7.1k views

ADD COMMENT • link updated 10.1 years ago by sascha-ott ▴ 10 • written 11.3 years ago by sanchezcavani ▴ 220

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Have you tried meme? http://meme.nbcr.net/meme/

ADD REPLY • link 11.3 years ago by Davy ▴ 410

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You can try matinspector (genomatix)

ADD REPLY • link 11.3 years ago by ancient_learner ▴ 680

score 2 · Answer 1 · 2013-08-28

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11.3 years ago

Istvan Albert 102k

Search this site for "motif search" for a number of answers.

ADD COMMENT • link 11.3 years ago by Istvan Albert 102k

score 0 · Answer 2 · 2014-10-17

In case you want 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