[Biojava-l] Problem with blast file parser

Richard Holland holland at eaglegenomics.com
Mon Jan 26 11:21:26 UTC 2009

This app looks hopeful for viewing blast output - haven't tried it


Otherwise, no there's no way of making Blast output in more than one
format at once. It's either text, or XML, but it won't do both.


Charles Imbusch wrote:
> Hello Mark,
> no I haven't tried to parse XML output from Blast.
> Just because of the fact that plain text output can be
> viewed with any editor. That's still very convenient.
> But I'm keen: is there actually an easy to use program for viewing
> XML output?
> Another option would be to generate XML and plain text
> output from Blast at the same time (in one run). But I couldn't find a
> way to do so. Maybe I missed something?
> Cheers,
>  Charles
> Mark Schreiber schrieb:
>> Have you tried parsing the XML output. While the text parser does
>> 'fake' XML by emitting SAX events I think that the XML parser may be a
>> lot more stable (the XML output of blast is more stable, at least
>> recently anyway).
>> I know this isn't the best solution to your problem but the default
>> text output of BLAST is not the most parseable. In fact it is probably
>> the least machine readable of all the blast outputs and definitely the
>> least stable.
>> - Mark
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Richard Holland, BSc MBCS
Finance Director, Eagle Genomics Ltd
M: +44 7500 438846 | E: holland at eaglegenomics.com

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