[EMBOSS] Remote Genbank from NCBI?

[Hans-Rudolf Hotz]

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 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:
>

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
>