[Biojava-l] grouped features using dazzle GFFAnnotationSource

Thomas Down td2 at sanger.ac.uk
Thu Jan 27 05:00:05 EST 2005

On 26 Jan 2005, at 19:55, Michael Heuer wrote:

> Hello,
> I would like to use the dazzle GFFAnnotationSource to display predicted
> transcripts on the Ensembl web interface, but it's a little bit 
> difficult
> to follow tags through from the GFF file to what ends up on the Ensembl
> web interface.
> I imagine I would want a row in the GFF file for each exon and then 
> group
> each exon together into a transcript using something in the tag/value
> field.  Does anyone have an example?

For Ensembl display, it should be sufficient to include a property 
named "id" on each GFF record -- all features with matching IDs will be 
grouped by the ensembl web-code.

Something like:

2L      annotation      exon       1       7528    0.0     .       0	id 
"Foo"; some_attribute "Bar"
2L      annotation      exon       9492    9835    0.0     .       0	id 

Should behave the way you want.


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