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!
Search this site for "motif search" for a number of answers.
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
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version 2.3.6
Have you tried meme? http://meme.nbcr.net/meme/
You can try matinspector (genomatix)