Database access for EMBOSS

[Peter Rice]

Claude Bonnard wrote:
> It is not very surprising that SRS is the  best mode  for a fast access
> to the sequence databases from EMBOSS. As I understood, the URL mode
> allows the access to a SINGLE sequence and would not support the
> "USA" standard (wild card query) as SRS mode does.

True. We could add an "SRSREMOTE" access mode to extend queries, easy to
program but maybe limited practical use.
 
> If it is the case, is there a solution when the SRS server is NOT
> on the same machine, but on a machine which is dedicated to SRS?
> I have in mind a rsh type of request and I would like to know if
> someone experience this type of problem and could help me in
> solving that.

SRS access mode allows you to define the name of the getz program.

How about an alternative name that is a script, and uses rsh to run a
remote getz and returns the results?

For example, if your script is called 'remotegetz' just add this to the
database definition:

app: remotegetz

(you can use the full path if needed)

Note: This was originally added because the Sanger Centre ran 2 versions of
SRS (5.1 and 6.0) and I needed to switch between them, but it has other
possible uses.


-- 
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Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at uk.lionbioscience.com +44 1223 224723