Genbank feature parsing performance

Khalil El Mazouari <[email protected]> Fri, 17 Jun 2011 11:16:11 +0200

Newsgroups	gmane.comp.java.bio.general
Message-ID	<[email protected]>

Hi,

I am developing an app where features are extracted from a large genbank file, and processed: multiple alignment, annotation....

The feature extraction is a real bottleneck in my app. It consumes 87% of total execution time. 

Feature extraction is done via:

FeatureFilter ff = new FeatureFilter.ByAnnotation(key, value);
FeatureHolder fh = richSequence.filter(ff);
Feature feat = fh.features().next();
...

Any suggestion on how to improve the performance of features extraction is welcome.

Thanks,

khalil
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