[Bioperl-l] conservative amino acid change?

[Heikki Lehvaslaiho]

I've modified Bio::Variation::AAChange by adding in similarity_score()
which returns an integer value from BLOSUM62 matrix. It then used by
the label() to classify single amino acid changes conservative or
nonconservative.

I am sure many people will find this definition controversial. If so,
please speak up. The BLOSUM62 based approach tries to be a maximally
generic way of defining this. (It is really frustrating to read
papers, even in Nature Genetics, talking about conservative changes
without defining the term at all.) If there is interest I am willing
to implement alternative ways of doing it. 

My implementation has the BLOSUM62 matrix inside the package. I can
not remember matrixes never being discussed in bioperl context. Other
bio* projects might have a selection of standard similarity matrixes
included. (?) Should we have them? And classes dealing with them?

... only after writing this I found blosum62.bla and gon250.bla from
examples directory...


	-Heikki

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     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
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