[Bioperl-l] conservative amino acid change?

[Heikki Lehvaslaiho]

Aaron J Mackey wrote:
> 
> You might also want to consider a special cloning method like "scale" to
> return a new copy of the matrix with a different scaling (than the
> default).  You might also consider a scale accessor method that reported
> the current scale.  It would also be nice to have a method to extract the
> information content (bits/residue) of the matrix.  Of course you'd need to
> have some letter frequencies lying around to do that - There are a handful
> of "standard" amino acid frequencies, it'd be great to get them into the
> repository for easy access.

Aaron,

Sound very good. Let's do it. Send them over.

> While not applicable to the BLOSUM series, many other matrices have an
> evolutionary rate matrix as their foundation (namely, PAM, JTT, WAG, etc).
> In this case you need only store one set of numbers, and dynamically
> generate the desired matrix at the desired scaling.  I have some code
> lying around to do this bit of black magic, if there's interest I'll
> send it along.

Please do. I'd be greatful.

> In summary, try to think of matrices as more living and breathing entities
> rather than just an organized bucket of numbers.  I'm sure this will mean
> that you'll want to build a Matrix::Factory and all that other stuff that
> makes using BioPerl difficult for us simpletons ;) ;)

Yet an other factory! Yee.

I've never seriously worked with similarity matrixes, but I'd like to
get this right. Please send me some recent review references and
pointers to above matrix acronyms and I'll see what I can put
together. 


/./././././


I knew was sticking out my neck when touching this topic. It was
deliberate. I've a few times brought it up in private discussion but
never got anywhere.
Last week I sent my sample code to a couple of friends who are
interested in this question and they also have started setting me
straight! Wonderful what a little piece of crappy code can do!

	-Heikki

 
> -Aaron
> 
> On Mon, 6 Aug 2001, Heikki Lehvaslaiho wrote:
> 
> > OK. I'll write the modules:
> >
> > Bio::Matrix::SimilarityMatrixI
> >       id()
> >       name()
> >       moltype()
> >       pam()
> >       max()
> >       min()
> >       def()
> >       deletion()
> >       similarity_score()
> >
> > Bio::Matrix::SimilarityMatrix
> > Bio::Matrix::SimilarityMatrixIO
> > Bio::Matrix::SimilarityMatrixIO::full
> > Bio::Matrix::SimilarityMatrixIO::half
> >
> > or something like that...
> >
> >
> > We'll need a data directory to place the default matrixes in. What
> > would be the best (platform independent) way of refering to files
> > within bioperl?
> >
> >       -Heikki
> > _______________________________________________
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> > Bioperl-l@bioperl.org
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> >
> 
> --
>  o ~   ~   ~   ~   ~   ~  o
> / Aaron J Mackey           \
> \  Dr. Pearson Laboratory  /
>  \ University of Virginia  \
>  /  (434) 924-2821          \
>  \  amackey@virginia.edu    /
>   o ~   ~   ~   ~   ~   ~  o
> 
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-- 
______ _/      _/_____________________________________________________
      _/      _/                      http://www.ebi.ac.uk/mutations/
     _/  _/  _/  Heikki Lehvaslaiho          heikki@ebi.ac.uk
    _/_/_/_/_/  EMBL Outstation, European Bioinformatics Institute
   _/  _/  _/  Wellcome Trust Genome Campus, Hinxton
  _/  _/  _/  Cambs. CB10 1SD, United Kingdom
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