[Biojava-l] Blast parser

[Susy Griffiths]

Hi,
I am trying to modify the BioJava cookbook example 'BlastParser' to 
process output from a Blast search.
I get the following exception when I run this with the output I have 
from the EBI web services NCBIBlast tool.
org.xml.sax.SAXException: Program ncbi-blastp Version 2.2.15 is not 
supported by the biojava blast-like parsing framework
at org.biojava.bio.program.sax.BlastLikeSaxParser.interpret 
(BlastLikeSaxParser.java:241)
at org.biojava.bio.program.sax.BlastLikeSaxParser.parse 
(BlastLikeSaxParser.java:160)

Also, are there BioJava tools to process the xml output rather than the 
raw Blast output?

many thanks,
Susy

-- 
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Dr S.L. Griffiths
YSBL
Department of Chemistry
University of York
Heslington
York
YO10 5YW
UK

http://www.pims-lims.org/
email: susy at ysbl.york.ac.uk
Tel. +44 (0)1904 328270
Fax +44 (0)1904 328266
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