[Bioperl-l] suggestion for a new module

[Heikki Lehvaslaiho]

Michaela,

The module does not exist. 

This is actually something to add into sequence retrieval logic.  Jason
posted a comment a while ago that modules in Bio::DB need cleanup but
no-one has volunteered.

This would be one more item to add.

The implementation should be generic enough to use any sequence revision
server. At the moment I know of two:

1. "Sequence Revision History"
http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi

2. Sequence Version Archive, SVA:
http://www.ebi.ac.uk/embl/sva/



I logged this as an enhancement request into the Bioperl Bugzilla:
http://bugzilla.bioperl.org/show_bug.cgi?id=1424

Using the Bugzilla highly recommended for all kinds of notes and bugs.

	-Heikki

On Wed, 2003-04-02 at 13:32, Mikaela Ilinca Gabrielli wrote:
> Hello everybody,
> 
> I was looking for a feature I hoped to find in Bioperl but I haven't found
> anything so I'd like to suggest the building of one.
> 
> It's about retrieving information on sequence status in NCBI databases.
> Biperl works fine for download of sequences and one gets the output in any
> format one wants. But(!), sometimes these sequences are no longer valid,
> they're just ghosts remaining in databases. This is very important
> information if you consider working with them. So I suggest a
> straight-forward way of retrieving that information. NCBI has already a
> "Sequence Revision History" - tool at
> http://www.ncbi.nlm.nih.gov/entrez/sutils/girevhist.cgi where sequences get
> status of 'dead', 'suppressed' or 'live'. It would therefore be great to
> parse such a result and retrieve the wanted status for a batch of sequences
> as a bioperl module complement.
> 
> I hope my point is undestandable.
> 
> If such a script already exists then I appologize for bothering you and ask
> you kindly to show me the way. It would simplify my life greatly at the
> moment.
> 
> Best regards,
> 
> Mikaela
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     _/  _/  _/  Heikki Lehvaslaiho          heikki at ebi.ac.uk
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