[Biojava-l] Sequence Iteration in BioJava(x)

Matthew Pocock matthew.pocock at ncl.ac.uk
Fri Dec 16 09:17:15 EST 2005

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.


> Regards,
> David
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