database info

[Peter Rice]

Koen van der Drift wrote:
> I want to try out some EMBOSS programs that use database searching. From 
> the docs it's not clear to me if and how I can search an online 
> database. My diskspace is limited, so I can't download a complete 
> database to my HD.

You can point the database definitions to a remote SRS server 
(srs.ebi.ac.uk usually) using access method SRSWWW

For example:

DB genbank [ type: N
    method: srswww format: genbank release: NCBI
    comment: "Genbank from NCBI"
    url: "http://cbr-rbc.nrc-cnrc.gc.ca/srs6bin/cgi-bin/wgetz"
  ]
DB embl [ type: N
    method: srswww format: embl release: EBI
    comment: "EMBL from EBI"
    url: "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz"
  ]


> Or maybe there is some small database available somwhere that I can use?

Yes ... there are databases defined in emboss.default.template with 
names tembl, tsw, and so on. These are small subsets of EMBL, SwissProt, 
etc. that we use for testing. The general principle is that any sequence 
used in the program documentation should appear there.

You can uncomment them, and set the value of emboss_tempdata to point to 
the share/EMBOSS/test directory where EMBOSS is installed (or the test 
directory in the source tree).

Hope this helps,

Peter Rice