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

[Schreiber, Mark]

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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