[Biojava-dev] Alignment algorithms

[mark.schreiber at group.novartis.com]

Hi -

I did some work on implementing SW and NW in biojava. It works pretty 
well. The only sticking point you will have is the substitution matrices. 
Some give scores for ambiguities which you need to be careful of. 
Ambiguities in Biojava are not atomic symbols but the substitution 
matrices treat them as if they are. It may actually be more realistic to 
just average the vaules of whatever the ambiguity is composed of.

Hopefully I can dig up the old code which I can submit as a basis. No 
promises. I suffered a HDD failure recently so it may have shuffled off 
this mortal coil.

- Mark





Rahul Karnik <rahul at genebrew.com>
Sent by: biojava-dev-bounces at portal.open-bio.org
10/03/2004 09:41 AM

 
        To:     biojava-dev at biojava.org
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-dev] Alignment algorithms


While reading through "Biological Sequence Analysis", I am finding it 
useful to reimplement some standard alignment algorithms in Java. 
Looking through the current Biojava package, I see that alignment is 
limited to HMM based methods. Would there be any interest in patches 
that add some standard alignment algorithms to the Biojava package? The 
ones I had in mind were Smith-Waterman (with substitution matrices), 
ClustalW and TCoffee. Along those lines, what would the appropriate 
package to use for such classes? And where should the substitution 
matrices go?

Thanks,
Rahul
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