On Dec 16 2005, Mark Fortner wrote:
Richard,
Thanks for the example. Your approach is very similar to a non-BioJava
approach that I had worked out earlier. I was wondering if the
BioJava(x) API provides any performance benefit over simply running a
window along a character stream?
The work that we're doing involves iterating through the human genome,
(and in a number of cases, metagenomic sequences) and we're trying to
squeeze as much performance out of it as possible while minimizing the
memory footprint.
The only case where I have encountered horrible performance out of using BJ
for this kind of activity is where the order is large (say >10). I think it
is killing the Alphabet code somewhere to represent the required alphabet.
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.
Regards,
David
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