[Bioperl-l] Circular genomes in Chado/BioPerl

Jim Hu 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  
parent feature.

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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