[Bioperl-l] SGD GFF3 file available soon

Jason Stajich jason at cgt.duhs.duke.edu
Wed Feb 18 17:30:45 EST 2004

Stan -

I am very much looking forward to this - up till now I have had to
reformat the .tab file myself just to get a working GFF3 where Bio::DB:GFF
aggregators would behave properly.  Looks like what you have for the
gene/CDS sets and will give it a try in my db/scripts.  Will be very happy
to see it all consolidated as you have done so nice work.

On Wed, 18 Feb 2004, Stan Dong wrote:

> Hi,
> I am a programmer at Saccharomyces Genome Database ( SGD,
> http://www.yeastgenome.org/ ). I am working on developing a flat file
> in GFF3 format ( http://song.sourceforge.net/gff3-jan04.shtml ) to
> represent sequence features of yeast genome and it will soon be
> released on our ftp site. This is very useful because quite a few open
> source softwares can take this file format as input such as Gbrowse,
> Chado
> I would like comments from people who are interested in doing similar
> things and those who have good/not-so-good experience on GFF3 to share
> with. For me, it took a while to get the specification done especially
> make the third column (type) fully compatible with Sequence Ontology
> (SO). One thing I liked about GFF3 is the last column (attributes)
> where you can put all kinds of useful information such as in our case
> GO annotation and a nice description of a feature. An example file of
> SGD GFF3 can be viewed here.
> ftp://genome-ftp.stanford.edu/pub/people/curator/GFF3Example.txt
> Thanks,
> Stan Dong
> Programmer, SGD
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Jason Stajich
Duke University
jason at cgt.mc.duke.edu

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