[Biojava-l] A problem parsing Blast XML output (blastN vs. blastP)

David Huen smh1008 at cam.ac.uk
Fri Nov 24 17:08:54 UTC 2006

On Nov 24 2006, Benoit VARVENNE wrote:

>I'm parsing blast results using biojava1.5 and a BlastXMLParserFacade with
>the code put at the end of this mail.
>I've tried this with a blastN query and there i got no trouble.
>However, i've tried to do exactly the same thing with a BlastP query and
>i've got the exception cited at the end of this mail.
> I've verified and the two infiles (blastn/blastp) seem to have the same 
> structures (except that one is for prot so data are different). (Please 
> find them as attached if you're used to this).
>Can someone help me ? I don't understand why it works in a case and not in
>the other one ...
I am uncertain whether BlastXMLFacade will actually support a protein 
sequence parse. It was originally developed to handle blastn. Anyone else 
tried it with blastp?

I'm offline till Sunday so I can't reply till then.

David Huen

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