[Bioperl-l] GFF3 and Gbrowse

Andrew Nunberg anunberg at oriongenomics.com
Tue Jun 28 11:21:26 EDT 2005

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

Andrew Nunberg
Orion Genomics

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