[Biojava-dev] Java implementation of Smith-Waterman algorithm

[Ahmed Moustafa]

In my implementation, I store the scoring matrices in a hash table of
2-dimensions arrays, the keys of the hash table are the names of the
scoring matrices e.g. BLOSUM62 and PAM250. I avoided using objects for the
scoring matrices to save the overhead of methods calling.

The Jar file contains about 70 scoring matrices from the NBCI site.

What do you think of keeping the Jar file as it is and writing a wrapper
class to interface between Biojava and JAligner?

On Tue, 14 Oct 2003, Schreiber, Mark wrote:

> Hi -
>
> Because we have traditionally used HMMs there where no scoring matrices per se, just transition and emission probabilities.
>
> A scoring matrix would be easy to acheive. I would suggest you start with an interface called ScoringMatrix that would have as a minimum methods like:
>
> String getName(); which would return Blosum60 or similar depending on the implementation.
> int getScore(Symbol s, Symbol substitute) which returns the int score for the substitution.
>
> You might want to also make a ScoringMatrixFactory that can generate appropriate instances of the ScoringMatrix from an XML file or files that could be included in the Distribution.
>
> - Mark
>
>
> 	-----Original Message-----
> 	From: Ahmed Moustafa [mailto:ahmed at arbornet.org]
> 	Sent: Tue 14/10/2003 6:45 p.m.
> 	To: Schreiber, Mark
> 	Cc: biojava-dev at biojava.org
> 	Subject: RE: [Biojava-dev] Java implementation of Smith-Waterman algorithm
>
>
>
> 	Hi,
>
> 	What are the Biojava's objects for the scoring matrices e.g. BLOSUMs and
> 	PAMs?
>
> 	Thanks,
>
> 	Ahmed
>
> 	On Mon, 13 Oct 2003, Schreiber, Mark wrote:
>
> 	> Hi -
> 	>
> 	> Probably just convert to use BioJava Symbol and SymbolList objects. Probably everything else is OK.
> 	>
> 	> - Mark
> 	>
> 	>
> 	> > -----Original Message-----
> 	> > From: Ahmed Moustafa [mailto:ahmed at arbornet.org]
> 	> > Sent: Sunday, 12 October 2003 7:06 p.m.
> 	> > To: Schreiber, Mark
> 	> > Cc: biojava-dev at biojava.org
> 	> > Subject: RE: [Biojava-dev] Java implementation of
> 	> > Smith-Waterman algorithm
> 	> >
> 	> >
> 	> > Hi Mark,
> 	> >
> 	> > I believe the current API is reusable. Is it necessary to
> 	> > convert the already existing implementation?
> 	> >
> 	> > Anyway, how can I convert my classes to biojava?
> 	> >
> 	> > Thanks!
> 	> >
> 	> > Ahmed
> 	> >
> 	> >
> 	> > On Sun, 12 Oct 2003, Schreiber, Mark wrote:
> 	> >
> 	> > > Hi -
> 	> > >
> 	> > > We have traditionally done pairwise alignments using HMMs. However
> 	> > > there have been numerous requests for an implementation of
> 	> > > Smith-Waterman. If you want some help coverting your classes to
> 	> > > biojava give us a yell on the list.
> 	> > >
> 	> > > - Mark
> 	> > >
> 	> > >
> 	> > >   -----Original Message-----
> 	> > >   From: Ahmed Moustafa [mailto:ahmed at arbornet.org]
> 	> > >   Sent: Sun 12/10/2003 9:19 a.m.
> 	> > >   To: biojava-dev at biojava.org
> 	> > >   Cc:
> 	> > >   Subject: [Biojava-dev] Java implementation of Smith-Waterman
> 	> > > algorithm
> 	> > >
> 	> > >
> 	> > >
> 	> > >   Hello,
> 	> > >
> 	> > >   I am working on a Java package of implementations of
> 	> > sequence alignment
> 	> > >   algorithms. I have released an implementation of Smith-Waterman
> 	> > >   algorithm with Gotoh's improvement. The time complexity
> 	> > is O(n2) and the
> 	> > >   space complexity is O(m * n + n) .
> 	> > >
> 	> > >   The package name is JAligner and it is hosted at sourceforge.net
> 	> > >   <http://jaligner.sourceforge.net>. There is a front-end
> 	> > demo using Swing
> 	> > >   and Java Web Start.
> 	> > >
> 	> > >   Could JAligner be incorporated into the BioJava project?
> 	> > >
> 	> > >   Best Regards,
> 	> > >
> 	> > >   Ahmed
> 	> >
> 	> >
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