[EMBOSS] Databases, additional info

[David Bauer]

Hi Ahmed,

If you do not want to install databases locally, you can get them from some servers, which are preconfigured in EMBOSS 6.4
You can see the lists of configured servers with "showserver".
If you need a sequence from embl, then then you can use the SRS server from the EBI.
In your case it would be:
"plotorf srs:embl:x13776"

If you are behind a http proxy you can add the proxy server in .embossrc in your home directory.
SET emboss_proxy  "your_proxy_server:port"
And if it needs authentication (only BASIC is usable)
SET emboss_proxy  "your_proxy_server:port Basic username:password"

David.
-----Ursprüngliche Nachricht-----
Von: emboss-bounces at lists.open-bio.org [mailto:emboss-bounces at lists.open-bio.org] Im Auftrag von Nabeel Ahmed
Gesendet: 16 July 2012 07:57
An: emboss at lists.open-bio.org
Betreff: [EMBOSS] Databases

I have recently installed EMBOSS-6.4.0 (Ubuntu 11.10).
I am unable to make it work directly with live databases (embl, uniprot) ,
working totally fine with local sequence files.
e.g

% *plotorf  *
Plot potential open reading frames in a nucleotide sequence
Input nucleotide sequence: *embl:x13776*

*Error:* Failed to open filename 'embl'**

Used 'showdb' , displayed table with zero rows.

Is there any configuration, i am missing??

Thanks
Ahmed
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