XML support in FASTA?

Aaron J Mackey ajm6q at virginia.edu
Tue Sep 18 11:04:07 EST 2001


We have been considering it for a long time, but have always become
"stuck" when considering which DTD to use, or modify for our own use.
BLAST's DTD is becoming more stable now, after its initial release, and
the fit is good, but not perfect, obviously.  We would love to see a more
generic "sequence analysis" or "search algorithm" DTD that could be
extended (and perhaps retrofitted for BLAST if there's enough consensus
and willingness).  There's also the issue that our group's research
interests and strengths are not in the creation of DTDs or other XML
schema, so we depend on the work of others more qualified to define "such
beasts".

So again, there is plenty of interest and willingness to support XML, but
we'd like to do it right, and we're just not entirely convinced how to do
that.

-Aaron Mackey
Graduate Student
William R. Pearson Laboratory

On 17 Sep 2001 greg.quinn at syngenta.com wrote:

> Does anyone know if there is planned any kind of support in the FASTA suite
> of programs for producing FASTA output in XML anytime soon? Does such a
> beast already exist?
> Thanks
> Greg
>
> ---
>
>

-- 
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/ Aaron J Mackey           \
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 \ University of Virginia  \
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