[Bioperl-l] Re: Bio::DB::EMBL

Rodrigo Lopez rls@ebi.ac.uk
Fri, 6 Apr 2001 08:53:08 +0100 (BST)

Hi Elia,

Sure. No disagreemen here. Today, with EMBL and GenBank we strive and
often disagree about what is it the user wants when he/she says fetch
embl:bum. The sequence in the official release? If there is an update, the
sequence in EMBLNEW? Or if there is an update to an update...and so
on...Without a sequence version server we always provide the latest
entry..although I for one would argue that it is sometimes better to
return a list if there is more than one entry (embl, emblnew++) in order
to allow the user to make a choice.


On Fri, 6 Apr 2001, Elia Stupka wrote:

> > There is another issue to take (or not) into account here: Until sequence
> > version servers are available it makes little sense to talk about them
> I don't really agree with this. Even if a certain server has one release,
> and thus one only version available, the user will still want to say give
> me AC000234.5, and don't give me anything if you don't have version 5. The
> reason behind this is, for example, golden path clones. If you are working
> off a static golden path, have a dataset related to a golden path, etc.
> you will not want to mess up your coordinate system by fetching the wrong
> sequence.
> Elia
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