[Bioperl-l] GFF3 and Gbrowse

Scott Cain cain at cshl.edu
Tue Jun 28 15:44:10 EDT 2005


This is the first I've heard of the so_transcript aggregator; have you
committed it anywhere?


On Tue, 2005-06-28 at 13:24 -0400, Lincoln Stein wrote:
> 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.
> Lincoln
> 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
Scott Cain, Ph. D.                                         cain at cshl.edu
GMOD Coordinator (http://www.gmod.org/)                     216-392-3087
Cold Spring Harbor Laboratory

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