Parsing blast results - Parsing with biojava failed with new NCBI blast (Nov/06/2006 )

Hi members,

I'm a new user of biojava and i've tried to use it to parse blast results (from NCBI nr database). I've already tried biojava1.4 and 1.5-beta but none of these seem to support the latest blast versions...

Can anyone help me with that ?

Thanks,
Best regards,
Benoît.

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use perl.

what EXACTLY are you trying to do? The more detail the better chance that someone can help... such an open ended question is a waste of your time as there are so many things you can parse from a blast report...

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Be sure i'm a Perl addict too but the choice has been made to use java this time !
I'm trying to parse Blast results in order to sort them (according to relevant parameters of e-value, length of alignment, ...) as to retrieve only good alignements of cDNAs on a genomic sequence.
This is the first step of the project.
The final aim is to analyze gene structures (using of course other resources and alignment tools).

Thanks for your answer,
I've now found the solution to my problem with biojava (if someone's interested let me know...)

Benoît.

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