[Biojava-l] Substitution matices

[Schreiber, Mark]

Actually this leads on to the issue of how the DP package does a
pairwise alignment between two protein sequences (or does it)? Does it
use some sort of PAM or BLOSUM matrix?

If it does could someone write a demo of it?

- Mark

> -----Original Message-----
> From: Matthew Pocock [mailto:matthew_pocock@yahoo.co.uk] 
> Sent: Friday, 10 May 2002 12:25 a.m.
> To: Schreiber, Mark
> Cc: biojava-l@biojava.org
> Subject: Re: [Biojava-l] Substitution matices
> 
> 
> Schreiber, Mark wrote:
> > Hi -
> > 
> > Does Biojava contain the concept of Substitution/ 
> similarity matrices?
> > 
> > If not should we put in an Interface (probably in the dp package)?
> > 
> > Probably containing the method:
> > 
> >   double substitute(Symbol a, Symbol b) throws 
> IllegalSymbolException;
> > 
> > Mark Schreiber
> > Bioinformatics
> > AgResearch Invermay
> > PO Box 50034
> > Mosgiel
> > New Zealand
> >  
> > PH:   +64 3 489 9175
> > FAX:  +64 3 489 3739
> 
> 
> Hi Mark,
> 
> Yes and no. There is no explicit substitution matrix 
> interface as such. 
> However a Count or Distribution over (e.g.) proteinXprotein will have 
> the desired properties. It is then a matter of interpreting the 
> distribution to be a substitution matrix, or the count as being 
> observations of substitutions.
> 
> Is there something (other than syntactic sugar) that isn't covered by 
> this approach?
> 
> Matthew
> 
> 
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