[Biopython-dev] Biopython's XMl parser fails with NCBI blast changed XML output format

Michiel Jan Laurens de Hoon mdehoon at c2b2.columbia.edu
Wed Jun 21 22:32:58 EDT 2006

I am not sure if the new XML format is really what NCBI wants it to be, 
since it does not agree with the Blast documentation. I asked NCBI about 
this; they have forwarded this question to their Blast developers, so 
hopefully we'll get a definite answer soon.
For the time being, I guess the only thing you can do is to download an 
older version of Blast and run your blast searches locally. Then, the 
blast XML output will be in the old format, and there should be no 
problem parsing them with the existing parser in Biopython.


Rohini Damle wrote:
> Hi,
> I am trying to parse the blast output (XML formatted, using online NCBI's
> blast) I got as a result for 'short nearly exact matches' for my 50-55 
> short
> protein sequences.
> It looks like the XML format has changed and biopython's XML parser 
> fails to
> parse the blast records.
> can somebody show a way to fix this thing?
> Thank you
> Rohini Damle

Michiel de Hoon
Center for Computational Biology and Bioinformatics
Columbia University
1130 St Nicholas Avenue
New York, NY 10032

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