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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