database info

[arun anirudhan]

Thank you very much for your valuable suggestion. I
have one problem now.
seqret embl:L07770 is giving result from embl website.
But is there a way to search embl site via a command
like this
seqret embl:insulin*
This is giving an error message 
Die seqret terminated: Bad value for option [sequence]
and no prompt.
Please help
Arun
 --- Peter Rice <pmr at ebi.ac.uk> wrote: > 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
>  

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