[DAS] GFF version in Spec

[Francis Ouellette]

On Mon, 7 Oct 2002, Cox, Greg wrote:

> Working through the DAS specification, there are two different versions of
> the GFF specification cited.  The "types" response indicates a GFF version
> of 1.0, while the "features" response calls for 0.95.  Muddying the waters,
> I found that the latest version of the GFF specification is 2.0
> (http://www.sanger.ac.uk/Software/formats/GFF/GFF_Spec.shtml).  I'm curious
> about two things; which version of GFF DAS should support, and what the
> available servers do support.  

We've come accross this GFF duality (tria-reality?) problem, and this
has basically made us shy away from using GFF. There is another
"stable" formats (table wise) that is documented and that will serve
our purpouse, like that used by Sequin:

http://www.ncbi.nlm.nih.gov/Sequin/table.html

which is what we are using:

Column 1: Start location of feature 
Column 2: Stop location of feature 
Column 3: Feature key 
Column 4: Qualifier key 
Column 5: Qualifier value 

and this is based on the feature table docs supported by
DDBJ/EMBL/GenBank which basically supports all we know, and use.

I understand that this is a limit that GFF tries to overcome 9ie,
only using DDBJ/EMBL/GenBank feature definitions, which lacks, for
example, gene finding program descriptors), but that wheel was
reinvented so many times that lack of agreement has made it difficult
for anybody (outside of the people who defined the new specs) to use.

regards,

f.



--
| B.F. Francis Ouellette             francis@bioinformatics.ubc.ca | 
| Director, UBC Bioinformatics Centre          Tel: (604) 875-3815 | 
| University of British Columbia               Fax: (604) 608-4795 | 
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