[Biojava-dev] Smith-Waterman algorithm

[jim.donohoe@earthlink.net]

Biojava developers:

Is anyone currently developing a sequence matcher using the Smith-Waterman
algorithm?  I wrote a quick and dirty implementation for an assignment in a
bioinformatics course (University California Santa Cruz, Extension), and I'm
considering developing an industrial-strength version as a course project over
the next few weeks.

I'm not yet familiar with the biojava architecture, and at this point I'm just
a beginner in biology, but I have a decent background in math and CSci and
several years of full-time Java experience.

My project would include:
	
	Use of the biojava architecture

	Needleman-Wunsch & Smith-Waterman algorithms

	Support for multi-threading

	Return multiple results, scored and sorted
	
Please let me know if this sounds useful, or if you have any other
suggestions--regarding this proposal or perhaps some other project--I'd like 
to hear them.

Thanks for your time,

Jim Donohoe
505 Cypress Point Drive #285
Mountain View, CA 94043
650-964-1193
jim.donohoe@computer.org