[Bioperl-l] What's the best object to store sequence assembly information?

[Allen Day]

Elia,

Would you happen to know where I can find the thread(s) for this topic? I
didn't turn up anything useful in the archive searching for 'assembly' or
'assemblies'.

-Allen


On Fri, 16 Aug 2002, Elia Stupka wrote:

> Dear David,
> 
> the short answer is we don't have a class yet for this. We had a long
> discussion about assemblies some time ago, but with no concrete
> conclusion. Mainly the discussion revolved around whether to handle
> multi-layer assemblies, or start off with basic ones first.
> 
> As in our community who codes it wins it you could start off by writing a
> simple object and interface for these assemblies, to kick-start the
> process.
> 
> >From the point of view of actually storing the assemblies in a database,
> we have recently made a generic feature database (GFD), which among other
> things could easily store assemblies as relationships between features
> (that are sequences) and sequences (if needed), so we'll be happy to
> assist in writing the necessary modules to store it.
> 
> Elia
> 
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