[EMBOSS] Remote Genbank from NCBI?

Georgios Magklaras georgios at biotek.uio.no
Sat Oct 1 09:37:50 UTC 2011

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 at 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:

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,

George Magklaras PhD
RHCE no: 805008309135525

Senior Systems Engineer/IT Manager
Biotek Center, University of Oslo
EMBnet TMPC Chair


Tel: +47 22840535

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