[Bioperl-l] Protein families

[Jason Stajich]

>
> 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.
>
> Bruno.
>
>
>
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>
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Jason Stajich
jason at bioperl.org