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#1
10-27-2011, 06:23 AM
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 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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| Tags |
| alignment , motif , motif search , protein , regex , searching , sequences , specific |
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