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

[Schreiber, Mark]

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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