Which example are you using?
The BlastEcho might be faster.
- Mark
Christian Köberle <[EMAIL PROTECTED]>
Sent by: [EMAIL PROTECTED]
01/20/2006 01:16 AM
To: bio java mailing list <biojava-l@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: [EMAIL PROTECTED]
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