Bioperl: SeqAlign BLAST parsing

Aaron J Mackey
Thu, 28 Oct 1999 08:03:45 -0400 (EDT)

On Thu, 28 Oct 1999, Catherine Letondal wrote:

> A very, very useful feature would just be to have an XML Blast output. XML documents
> are easy to parse, and benefit from a wide range of tools, __which allow to
> build custom parsers__ at a little cost. Several biologists here at Pasteur
> have already asked us (the computing center) about such a feature.

Catherine, you are totally correct.  According to Lincoln at the BioPerl
conference, Warren Gish is willing and ready to put XML output options
into WU-blast, and I know that Bill Pearson is willing and ready to put
XML output options into the entire FASTA package.

What Bill would really like to see is unified DTD for both BLAST and FASTA
(and their various children algorithms).  Since you have already written a
FASTA DTD, and know the location of the BLAST DTD, I propose that we all
work together on making this a reality, sooner rather than later.


 o ~   ~   ~   ~   ~   ~  o
/ Aaron J Mackey           \
\  Dr. Pearson Laboratory  / 
 \ University of Virginia  \     
 /  (804) 924-2821          \
 \    /
  o ~   ~   ~   ~   ~   ~  o

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