[Bioperl-l] Circular genomes in Chado/BioPerl
js5 at sanger.ac.uk
Mon Sep 8 16:13:12 EDT 2008
On Mon, 8 Sep 2008, Jim Hu wrote:
> In discussions with GMOD about Gbrowse, we've come up with a proposal for
> handling circular genomes and features that cross the origin in such genomes.
> This applies to lots of prokaryotic and viral genomes, and might be valuable
> for some ways of representing terminally redundant linear genomes.
> 1) Keep the requirement that start < end
> 2) allow end > parent feature length
> 3) parent feature gets an is_circular boolean
> 4) use modular arithmetic to calculate the real position of end on the parent
This is how we are considering handling features in Ensembl as well (the
Ensembl genomes project will be setting up websites for bacterial and
> We'd like to do this in a way that will be consistent with Chado and BioPerl
> representation of features as much as possible (realizing that there is the
> usual interbase or not coordinate issue). What do people think? Lincoln is
> on board for modifying the GFF3 spec.
> Jim Hu
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> Bioperl-l mailing list
> Bioperl-l at lists.open-bio.org
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