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.
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