[Bioperl-l] Circular genomes in Chado/BioPerl

James Smith 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 
> feature.

This is how we are considering handling features in Ensembl as well (the 
Ensembl genomes project will be setting up websites for bacterial and 
viral genomes)


>
> 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.
>
> Thanks!
>
> Jim Hu
>
> =====================================
> Jim Hu
> Associate Professor
> Dept. of Biochemistry and Biophysics
> 2128 TAMU
> Texas A&M Univ.
> College Station, TX 77843-2128
> 979-862-4054
>
>
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