[Open-bio-l] EMBL/Genbank pass-thru proxy for Bio::DB::GFF

[Lincoln Stein]

Hi All,

The Bio::DB::GFF module now has an adaptor called "biofetch", which is a 
pass-thru proxy for Genbank/EMBL.  If the caller requests a landmark of type 
"Accession" and the landmark isn't found in the local database, the module 
uses the biofetch accessor to fetch and parse the corresponding Genbank/EMBL 
entry.  The entry is then stored into Bio::DB::GFF for use later.

The upshot of this is that GBrowse can now be used as a simple visualization 
front end for the entry databases.  To see how it works, try this:

	http://www.wormbase.org/db/seq/gbrowse?source=embl

I've only tried loading BAC and organelle-sized entries so far.  It will 
undoubtedly take a LONG time to parse an arabidopsis chromosome, let alone a 
vertebrate.

Another unresolved issue is how to check for updates.  Currently this doesn't 
happen.  However it should work properly if you request a dotted accession 
number.

It seems to me that an on-demand loader would be very useful with BioSQL, no?

Lincoln