[EMBOSS] refseq IDs via SRSWWW

[Peter Rice]

F.J. Novo wrote:

> Hello, I've just configured a remote access to genbank in my 2.8.0 
> installation, as suggested:
> 
> 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"
> ]
> 
> It works fine with EMBL-type accession nos. (AJXXXXXX), but it seems 
> unable to retrieve refseq IDs (NM_XXXXX). Am I missing something?

srswww will query by id and acc.

You can query a remote SRS database for any ID or ACC value.

If you define some extra fields, you can query by description, organism 
and keyword.

The NM_xxxxx codes are NCBI's REFSEQ identifiers. GenBank entries may 
refer to them, but they are not indexed by them.

At the Canadian SRS server, the REFSEQ DNA entries are in REFSEQNT so 
you can define that as a database (use dbalias:refseqnt in the EMBOSS db 
definition if you want to use another database name locally)

We have considered providing an Entrez access method to try retrieving 
these strange identifiers (refseq, GI numbers, and so on) from NCBI but 
(a) they change the Entrez interface each time I look and (b) it 
requires far too much rewriting of parsers each time to get to the 
actual entries. Some day, if it becomes stable and if one can query byu 
such fields and get straight to the entries then we may implement it.

Hope this helps,

Peter Rice