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

[Thomas Down]

On Sat, Aug 17, 2002 at 07:28:07AM +0000, borg collective wrote:
> Is there a Java implementation of Smith-Waterman algorithm available on 
> biojava?  I was not able to find any reference to it in the documentation.  
> If there isn't one, does anyone know where I can obtain the source code for 
> one?  Thanks

Hi Borg.

The BioJava package includes a dynamic programming library,
with which is it possible to implement a range of sequence
alignment algorithms, including basic Smith-Waterman, plus
more sophisticated variants (affine gaps, multiple match states
for aligning different classes of sequence, etc.).  If you
download the source distribution, you should find an example:

     demos/dp/PairwiseAlignment.java

Most of the DP code was written by Matthew Pocock, who might
be able to help out if you've got any questions.

     Thomas.