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/ ============================================================ _______________________________________________ EMBOSS mailing list EMBOSS@lists.open-bio.org http://lists.open-bio.org/mailman/listinfo/emboss