[EMBOSS] EMBOSS remote server list?

[Peter Rice]

Hi Ashika,

>  url: "http://mrs.cmbi.ru.nl/mrs-web/entry.do?db=genbank_release&id=%s"
>
> Error: Failed to read sequence 'genbank:AJ972404'
> Error: Failed to read sequence 'genbank:AJ972403'
> Error: Failed to read sequence 'genbank:CAAA01078923'
> Error: Failed to read sequence 'genbank:CAAA01073483'
> 
> Error: Failed to read sequence 'genbank:10129688'
> Error: Failed to read sequence 'genbank:1054739'
> Error: Failed to read sequence 'genbank:112004011'
> Error: Failed to read sequence 'genbank:1136277'
> 
> Where can i find a server which has all this data?

Those look like NCBI "GI numbers" to me. These are only in Genbank, not
in the EMBL versions of the same entries.

Although MRS can search by GI number in the web interface, we need a URL
that can query by GI number and return the entry.

A further issue is that MRS servers are changing to MRS version 4 so
their interfaces could change.

The URLs for all these database servers can change. Here is one for
Entrez at NCBI that worked today:

DB gigenbank [ type: N method: url format: genbank
    url: 
"http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nuccore&id=%s&cmd=text"
    comment: "Genbank GIs" ]

This will retrieve the entries you listed.

> I tried some other servers in 
> http://downloads.lionbio.co.uk/publicsrs.html  and most of the 
> servers didnt give results to the latter ids (10129688-113627).

That is an SRS 8 server. We are waiting for information from SRS8
support on a good URL to use to get ASCII (normal text format) entries.
meanwhile we support SRS 7 servers especially the srs.ebi.ac.uk server.

Does anyone have suggestions for SRS8 server access?

regards,

Peter