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ParkaDude 10-27-2011 06:23 AM

Searching a specific motif in protein sequences
 
Hi there,

I nedd help since I'm a little bit lost here...

So, here is my problem:

- I have some protein motifs expressed as regexes, e.g. A(BC|CD|DF)GHIL(X)MN

- I have a number of specific fixed sequences.

- I have to find if the the motifs are present in the sequences (possibly through alignment)

Which tool should I use? So far I found "Protein Pattern Search", I can not link the direct website since as new user I'm not allowed to post URLs.

(it's geneinfinity.org/sms/sms_protpatterns. html)

The point is that the tool is looking for exact matches, while I basically want to align the protein sequences with the motifs and see how they fit, maybe the just partially align but that's ok.

I founnd a lot of searching algorithm but they all use known (not-customizable) motifs, or they require markov models (while I just have regexes).

Any suggestion?


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