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

[Elia Stupka]

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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