On Friday 16 December 2005 09:25, David Huen wrote: > > If that is the kind of case you want to deal with, I would believe the > SSAHA code in BJ may be adapted to your purposes but this comment does not > arise from direct personal experience.
The biojava SSAHA code is likely to be quite efficient for this kind of sliding-window application. I think it can be attached directly to the sequence IO events, and encodes the DNA n-mers directly as bits in an integer datatype. All operations are done by integer comparison, logical operations and shifts. Even though SSAHA itself is probably not what you want, nearly all the building blocks should be there in that module. Matthew > > Regards, > David > _______________________________________________ > Biojava-l mailing list - Biojava-l@biojava.org > http://biojava.org/mailman/listinfo/biojava-l _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
