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).