[Bioperl-l] GFF3 and Gbrowse

Lincoln Stein lstein at cshl.edu
Tue Jun 28 13:24:42 EDT 2005

The bioperl GFF database (both the inmemory and relational database versions) 
need to be brought up to date to handle the full expressive powerof GFF3. So 
for the time being ID trumps Name. Also you must use the so_transcript 
aggregator instead of the processed_transcript aggregator.


On Tuesday 28 June 2005 11:21 am, Andrew Nunberg wrote:
> I was wondering if there is any documentation about using GFF3 format with
> Gbrowse.  Since this is the "new" format, I wanted to start using it, but
> observing some behaviors.
> The GFF3 documentation on http://song.sourceforge.net/gff3.shtml indicates
> the Name tag is the id to be displayed and the ID tag is unique and
> internal, however when I use Gbrowse 1.62 it is ID that is being displayed
> as the label.
> I wish to use processed_transcript aggregator, the GFF3 document indicates
> you only need to  display the exons and CDS and the UTRs will be inferred,
> however I did not see that when  viewed in Gbrowse.
> If there is some extra code or documentation I need please let me know
> Thanks
> Andy

Lincoln Stein
lstein at cshl.edu
Cold Spring Harbor Laboratory
1 Bungtown Road
Cold Spring Harbor, NY 11724
(516) 367-8380 (voice)
(516) 367-8389 (fax)

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