[Bioperl-l] split seq feature and fuzzy feature proposal

[gert thijs]

Hilmar Lapp wrote:
> 
> Yeah, that's the really hairy case. We probably should define
> first what we would like to be able to do with compound locations.
> This is a strong call for feedback: what do people out there using
> the package intend to do with compound locations? E.g. if you draw
> annotations, would you just draw the part referring to the
> attached seq? Ensembl people, any experience/wishlists for this?
> 

I hope do not mind me giving some comments on this issue.
I am writing some programs to automatically extract genes and intergenic
regions from DNA sequences. So, I am mostly interested in the type of a
feature and also its start and end position in the sequence. The main problem
I am facing is that sometimes a feature is not extracted from the sequence
because it has a fuzzy location. 
eg. if the location of a CDS is described as "join(AL101010.1:1..201,123..245)
this CDS is not add to the list of feature and it is impossible to do anything
usefull with this sequence for me. 
In my opinion, I think it is important that a feature is created even if the
location is fuzzy. When there is a problem, it should be possible to access
the description of the location.

Gert



-- 
+ Gert Thijs              
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