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

[David Huen]

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