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 _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
