[Bioperl-l] gff2xml

Torsten Seemann torsten.seemann at infotech.monash.edu.au
Mon Jun 18 21:26:41 EDT 2007


(Sean, please reply to the bioperl-l list rather than to me personally
so everyone can read it. i'm reposting it here)

> > I posted this on the gbrowse list earlier. I'm looking to convert gff
> > data files into xml. Does anyone know of a module written to do this
> > already?
>
> What DTD do you want the XML to conform to?
> eg. ChadoXML, TinySeq XML, TIGR XML ... ?

Hi Torsten,
I'm collaborating with other groups and want web-service compatible
functionality for various tools. Normally the analysis tools I'm using
generate gff output. I'm going to have to wrap this output in XML with
XSL stylesheet for end-users to view. Haven't done it before and don't
know what DTD to use. The bp_seqconvert.pl doesn't accept gff format.
I would imagine the DTD would be quite short as the gff files are very
standard, I just don't have any experience with these DTD
requirements.
--Sean O'Keeffe <limericksean at gmail.com>


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