[EMBOSS] Databases

[Georgios Magklaras]

Hi Nabeel,

I made this guide on the subject of EMBOSS databases:

http://epistolatory.blogspot.no/2012/08/the-bioinformatics-sysadmin.html

I hope it explains the things you need to know to get started.

GM

Best regards,

-- 
-- 
George Magklaras PhD
RHCE no: 805008309135525
  
Senior Systems Engineer/IT Manager
Biotechnology Center of Oslo and
the Norwegian Center for Molecular Medicine
EMBnet TMPC Chair

http://folk.uio.no/georgios

Tel: +47 22840535



On 07/16/2012 01:05 PM, Peter Rice wrote:
> 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
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>