[EMBOSS] Databases

[Peter Rice]

On 16/07/2012 06:56, Nabeel Ahmed wrote:
> 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.

That is very strange.

EMBOSS 6.4.0 includes a set of installed databases which should appear 
in showdb.

One of these is the data resource catalogue (drcat) which in turn 
defines the embl database for web access.

David Bauer has already explained how to get web access working if you 
have a proxy to go through, but that does not explain the empty showdb 
output.

With drcat defined in a standard installation, and web access, you 
should already have access to the embl database (it will not appear in 
the showdb output of a standard installation, but is reachable by a 
lookup in DRCAT).

Could you please try the command

embossversion -full

which should include the value of Emboss_Standard. In this directory you 
should have a file emboss.standard that defines drcat, several other 
databases, and the servers that David Bauer mentioned.

My first guess would be that there is some problem with access 
permissions to that file.

regards

Peter Rice
EMBOSS Team