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

[Ahmed Moustafa]

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