[Biojava-l] FW: Location Problems

[David Huen]

On Tue, 23 Oct 2001, Cox, Greg wrote:

> There's a architectural problem with how locations are represented.  The
> problem is that strandedness is applied at the feature level, but in some
> genbank files applies at the sub-location level.  For example, MUSPRCON01
> has the feature:
> 
>      gene            join(complement(244..1502),L21211.1:1..105,
>                      L21222.1:1..141,L21212.1:1..89,L21213.1:1..101,
>                      L21214.1:1..185,L21215.1:1..225,L21216.1:1..113,
>                      L21217.1:1..116,L21218.1:1..130,L21219.1:1..198,
>                      L21223.1:1..137,L21220.1:1..141,L21221.1:1..664)
>                      /gene="PC4"
> 
> 	This highlights two things; first, remote feature probably has to be
> re-worked.  It has no concept of strand, and should.  The other is that
> there's at least one case where some component parts of a compound location
> are on different strands.
> 
> 	I'm not making any proposals right now, just highlighting the
> problem.  Let me know if you have brilliant thoughts.
> 
Isn't this sequence representable with ComponentFeatures?  At least I use
them to effect mappings of this kind in Ragbag.  Or have I missed the
point completely 9quite possible)?

David Huen