Question: How Can I Find Specific Motifs Of Promoter Sequences Of A Large Number Of Genes
1
gravatar for sanchezcavani
5.6 years ago by
sanchezcavani210
Canada
sanchezcavani210 wrote:

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 • 4.3k views
ADD COMMENTlink modified 4.5 years ago by sascha-ott10 • written 5.6 years ago by sanchezcavani210
1

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

ADD REPLYlink written 5.6 years ago by Davy360

You can try matinspector (genomatix)

ADD REPLYlink written 5.6 years ago by ancient_learner610
2
gravatar for Istvan Albert
5.6 years ago by
Istvan Albert ♦♦ 80k
University Park, USA
Istvan Albert ♦♦ 80k wrote:

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

ADD COMMENTlink written 5.6 years ago by Istvan Albert ♦♦ 80k
0
gravatar for sascha-ott
4.5 years ago by
sascha-ott10
United Kingdom
sascha-ott10 wrote:

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

ADD COMMENTlink written 4.5 years ago by sascha-ott10
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