XML support in FASTA?

Keith James kdj at fes1.sanger.ac.uk
Tue Sep 18 11:04:05 EST 2001

>>>>> "Greg" == greg quinn <greg.quinn at syngenta.com> writes:

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

I don't know about support within Fasta (I just grepped for xml in the
source + docs of the latest version and found no mention, so I assume
nothing is imminent).

I wrote a parser for the -m 10 Fasta format for the BioJava
project. This can be coupled to the project's framework for generating
SAX events to a common DTD for Blast, Fasta and HMMER. There are event
listeners provided which emit XML (no coding required).

See http://biojava.org if you are interested. If it looks useful to
you but you can't find what you need on the site, feel free to drop me
a line.



-= Keith James - kdj at sanger.ac.uk - http://www.sanger.ac.uk/Users/kdj =-
The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambs CB10 1SA

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