[Bioperl-l] How to express 'histogram' data in GFF3

Matthew Vaughn vaughn at cshl.org
Fri Mar 18 06:55:20 EST 2005

OK, I've bashed my head against this and have come up short, so now I'm 
asking for help. Recently, I decided to upgrade my development system 
to BioPerl 1.5 and bring all my code up to GFF3 compliance. This of 
course, includes code that generates GFF files for loading into our 
local Generic Genome Browser (1.62).

The problem comes when I try to express histogram data. In the past, 
rows like this worked fine as GFF2

"ChrII	rev1	poly1	1591004	1591068	464.835	-	.	poly1 ChrII:rev1"

but this is invalid for GFF3. As far as I can figure from interpreting 
the GFF3 spec, the same record should look something like this

"ChrII	rev1	poly1	1591004	1591068	464.835	-	.	ID=poly1%3AChrII%3Arev1"

But this violates the GFF3 spec in that ID is now non-unique. Rows 
formatted thusly also fail to display any histogram data in my browser.

I've considered loading the array data as GFF2 and my annotation data 
as GFF3, but that seems, well, inelegant (plus I don't even know if 
that will work)

Any input will be very much appreciated!


Matthew W. Vaughn, Ph.D.
Cold Spring Harbor Laboratory
Delbruck Laboratory / Martienssen Group
1 Bungtown Road
Cold Spring Harbor, NY 11724

phone: (516) 367-8469

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