On 10/01/2011 11:37 AM, Georgios Magklaras wrote:
On 09/30/2011 08:22 PM, Ed Siefker wrote:
Is there a way to access NCBI Genbank remotely?
My emboss.default contains the following:
DB tgb [ type: N method: srswww format: genbank
url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz";
dbalias: genbankrelease
fields: "sv des org key"
comment: "Genbank IDs" ]
However that server does not exist. I've looked on
the NCBI website for alternatives, but all I can find
is the ftp site. I've also read the EMBOSS admin guide.
The examples there use infobiogen.fr, which is also
closed.
So what do people do for genbank access? I'd prefer
to avoid setting up a local database myself if I can.
Is there a list of genbank mirrors around somewhere?
_______________________________________________
EMBOSS mailing list
EMBOSS@lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss
Hi Ed,
Yes, that SRS server does not exist anymore. The EBI SRS server is there
and updated regurarly, but I am not sure if it offers Genbank. It does
offer a full version of EMBL (nucleotide database, the contents of the
release should mirror sync those of Genbank), so if you type the
following in your emboss.default file, you will connect:
Try the SRS server at the 'DKFZ', see:
http://www.dkfz.de/menu/cgi-bin/srs7.1.3.1/wgetz?-page+databanks
or check the list of Public SRS Installations, see:
http://www.biowisdom.com/download/srs-parser-and-software-downloads/public-srs-installations/
(although, I am not sure whether this list is actually still maintained)
Regards, Hans
DB embl [ type: N method: srswww format: embl
url: "http://srs.ebi.ac.uk/cgi-bin/wgetz";
fields: "id sv des org key"
comment: "EMBL" ]
Best regards,
GM
_______________________________________________
EMBOSS mailing list
EMBOSS@lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/emboss
