[Biojava-l] Database search with Smith and Waterman

[Peter S]

Dear All, 

I'm looking for an implementation of Smith and Waterman algorithm to use in the Java desktop application I want to develop. 

I did find some information on pairwise aligners but what I would ideally want to have is something similar to the SSEARCH package that can perform alignments against a very big databases, saved locally in a fasta format. Speed is quite important and ideally I would need an output that I can easily parse, identifying mismatch/gap positions etc.

Any suggestions if there is any java implementation that would fit the description? I will be working on short sequences so sensitivity is crucial. 

Thanks very much for your help,
Peter