[Bioperl-l] [Gmod-schema] Circular genomes in Chado/BioPerl

Chris Fields cjfields at illinois.edu
Tue Sep 9 14:49:13 EDT 2008


Sent just a bit too early!

On Sep 9, 2008, at 1:24 PM, Chris Fields wrote:

> Is there any particular reason we don't treat this similarly to the  
> way BioPerl does, which is to simply treat the origin-overlapping  
> feature as a split location?  GenBank treats this similarly.  For an  
> faux example, the bug I just fixed for bugzilla has one:
>
> http://bugzilla.open-bio.org/show_bug.cgi?id=2579
>
> An actual GenBank case is the Sulfolobus solfataricus genome  
> (NC_002754), and I'm sure Jim could come up with more.  The only  
> caveat is whether we should represent this

... as a 'special case' for features overlapping the origin in a  
circular sequence.

> As for multiple revolutions, I'm not sure the hand-wringing about  
> specifics is worth it unless we have explicit workable examples to  
> test against (preferably examples which would potentially pop up),  
> but Lincoln's proposal sounds fine.
>
> chris




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