[EMBOSS] accessing remote databases

[Hamish McWilliam]

Hi Iddo,

> Since the SRS server at EBI was retired, I am looking for other remote
> databasest to accessvia EMBOSS. The DKFZ server seems to do a mostly good
> job (although slow from where I'm at):
> 
> http://www.dkfz.de/menu/cgi-bin/srs7.1.3.1/wgetz
> 
> However, I was wondering how to access genbank via EMBOSS (thorugh any
> protocoal) , what would be the entry in .embossrc?
> 
> Also, are there SRS servers I can use in N. America that would hopefully be
> faster?

For details of public SRS servers, see the "Public SRS Installations" at:

http://bioblog.instem.com/download/srs-parser-and-software-downloads/public-srs-installations/

Current versions of EMBOSS come with a number of data sources configured
which are accessed via the data server support. You can see details of
the configured servers using the showserver command:

http://emboss.sourceforge.net/apps/release/6.6/emboss/apps/showserver.html

And you can access entries via these services by using the slightly
extended USA which specifies the server as well as the database, for
example:

entret -stdout -auto dbfetch:embl:L12345

to get EMBL-Bank data from dbfetch, or to get the same entry from NCBI
Entrez:

entret -stdout -auto entrez:nucleotide:L12345

Since NCBI's GenBank is part of the INSDC (http://www.insdc.org/), the
data in GenBank is also available in ENA EMBL-Bank and DDBJ. So you
could use the existing server definitions containing EMBL-Bank or DDBJ.

Alternatively you can define your own (see
http://emboss.open-bio.org/html/adm/ch04s01.html) to access GenBank via
NCBI's E-Utitlites (http://eutils.ncbi.nlm.nih.gov/), for example:

# NCBI GenBank+RefSeq via NCBI Entrez
DB nucleotide [
   type: nucleotide
   method: entrez
   format: genbank
]

Since NCBI have also recently released command-line clients for their
E-Utilities Web Services
(http://www.ncbi.nlm.nih.gov/news/02-06-2014-entrez-direct-released/)
another option would be to use these directly or wrap them as EMBOSS
database definitions for your commonest queries.

All the best,

Hamish
-- 
============================================================
Mr Hamish McWilliam,
Web Production,
European Bioinformatics Institute (EMBL-EBI),
European Molecular Biology Laboratory,
Wellcome Trust Genome Campus,
Hinxton, Cambridge, CB10 1SD
United Kingdom

URL: http://www.ebi.ac.uk/
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