[Bioperl-l] Protein families
vecchi.b at gmail.com
Wed Feb 11 16:37:52 EST 2009
Thanks! Coincidentally, after submitting my question I found about HMMER. It
seems to be the right tool, and It also has a BioPerl module to parse its
2009/2/11 Jason Stajich <jason at bioperl.org>
>> The simplest way that I can think of for doing this is to first
>> build a profile for the family, based on a multiple sequence
>> alignment; then to align each random sequence against the profile and
>> calculate an e-value. But since I don't know much about this things, I
>> really can't judge whether it makes sense or is completely wrong.
>> Using Bio::Tools::HMM sounded fine, but unfortunately it doesn't offer
>> a method for calculating the probability of an observation sequence,
>> given the profile.
>> I'm not entirely sure about the whole problem you describe but if you are
> using HMMER for this - "hmmsearch" does give you e-value of similarity of
> sequence to the profile - you need to do the hmmcalibrate beforehand though
> - this is covered in HMMER user manual.
> What would you suggest? Thanks in advance!
>> PS: If there is a more appropriate mailing list for this sort of
>> questions, please don't hesitate to educate me.
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> Jason Stajich
> jason at bioperl.org
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