[Bioperl-l] SGD GFF3 file available soon

Stan Dong qdong at genome.stanford.edu
Wed Feb 18 17:09:27 EST 2004


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 etc.

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.



Stan Dong
Programmer, SGD

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