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FlyBase gene models displayed as remote tracks on Gbrowse, via gbgff

gbgff is a GFF3 dumper script that comes packaged with GBrowse version 1.69 and later.  Its purpose is to export configured annotations from one instance of GBrowse to another.

  • It is analogous to DAS, except that:
    • It supports both server and client-side configuration of glyph rendering
    • It supports 3-level gene models and other multi-level features made possible by GFF3


  • gbgff does not require any special set-up - it is installed with GBrowse.
  • This application has only been tested with servers using a GFF3 back-end with Bio::SeqFeature::Store



  • Tracks are configured as normal (see the GBrowse2 Admin Tutorial and the GBrowse Configuration HOWTO for details)
  • The config stanza for each feature type is dumped with the GFF3
  • The only thing to be aware of is that callbacks are disabled for security reasons
    • Any server-side options configured with callbacks will fall through to the [TRACK DEFAULTS] setting, if available
    • Note: server-side options will be overridden by client-side settings, so callbacks can still be used


  • The GFF3 exported by gbgff can be used like a DAS source.

as a DAS-lite remote feature

  • to use the dumper as a DAS source, add the remote feature option

The URL format follows the same pattern as GBrowse: host/cgi-bin/gbgff/data_source?type=type1+type2;ref=$ref;start=$start;end=$end

remote feature =;ref=$ref;start=$start;end=$end
glyph          = gene
bgcolor        = blue
  • Note1: that the $ref, $start, and $end variables are interpolated to the current segment
    • These variables are a required part of the url
  • Note2: any options specified in the client-side config file will override remote options specified on the server

as a remote URL

  • To use as a remote uploaded URL, enter a URL with the same structure as above into the "remote URL" box on the GBrowse display

Gff remote url.png

  • which will yield a new track:

Gff remote track