[Bioperl-l] Circular genomes in Chado/BioPerl
jimhu at tamu.edu
Mon Sep 8 14:44:22 EDT 2008
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
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.
Dept. of Biochemistry and Biophysics
Texas A&M Univ.
College Station, TX 77843-2128
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