[Biojava-l] Parse XML BLAST

[mark.schreiber at novartis.com]

Which example are you using?

The BlastEcho might be faster.

- Mark





Christian Köberle <koeberle at mpiib-berlin.mpg.de>
Sent by: biojava-l-bounces at portal.open-bio.org
01/20/2006 01:16 AM

 
        To:     bio java mailing list <biojava-l at biojava.org>
        cc:     (bcc: Mark Schreiber/GP/Novartis)
        Subject:        [Biojava-l] Parse XML BLAST


Hi,

is it possible to get the information form BLAST-XML Tag  <Hit_def> 
with bioJAVA?

I use the example from  BioJava In Anger for parse a BLAST.
I use BlastXMLParserFacade as a parser.
To get the definition of the target gen I use 
SeqSimilaritySearchHit-Object parse the result from getSubjectID() and 
download the Sequence from NCBI. But this is very slow.

for (Iterator k = result.getHits().iterator(); k.hasNext(); ) {
          SeqSimilaritySearchHit hit = (SeqSimilaritySearchHit)k.next();
          String name = hit.getSubjectID().split("\\|")[3];
          Sequence seq = db.getSequence(name);
          System.out.print("\t" + 
seq.getAnnotation().getProperty("DEFINITION"));
}

Is there are a better way to get the Information?

thanks,
Christian

-- 
Christian Köberle

Max Planck Institute for Infection Biology
Department: Immunology
Schumannstr. 21/22
10117 Berlin

Tel: +49 30 28 460 562
e-mail: koeberle at mpiib-berlin.mpg.de

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