[EMBOSS] Remote Databases and possibly drcat

[Citron, Bruce A.]

What do I need to do, or have our IT guy adjust, to be able to grab sequences from ncbi (genbank, refseq, etc.) into my directory on a LINUX mainframe?  This used to work under GCG via net fetch.  I'm using EMBOSS 6.6.0.0, command line.

I can use seqret to grab embl sequences (seqret embl:accession) and that works fine, however none of the synonyms that I can think of for genbank work.

Should our system have access through drcat?  I do see Genbank, and many other remotes listed there.  I'm not sure how that works.

I'm also not sure why it accesses embl sequences because embl isn't listed by showdb.

showdb produces:
Display information on configured databases
# Name          Type     Comment
# ============= ======== =======
taxon           Taxonomy NCBI taxonomy
drcat           Resource Data Resource Catalogue
chebi           Obo      Chemical Entities of Biological Interest
eco             Obo      Evidence code ontology
edam            Obo      EMBRACE Data and Methods ontology
edam_data       Obo      EMBRACE Data and Methods ontology (data)
edam_format     Obo      EMBRACE Data and Methods ontology (formats)
edam_identifier Obo      EMBRACE Data and Methods ontology (identifiers)
edam_operation  Obo      EMBRACE Data and Methods ontology (operations)
edam_topic      Obo      EMBRACE Data and Methods ontology (topics)
go              Obo      Gene Ontology
go_component    Obo      Gene Ontology (cellular components)
go_function     Obo      Gene Ontology (molecular functions)
go_process      Obo      Gene Ontology (biological processes)
pw              Obo      Pathways ontology
ro              Obo      Relations ontology
so              Obo      Sequence ontology
swo             Obo      Software ontology

# Name          Type     Comment
# ============= ======== =======
taxon           Taxonomy NCBI taxonomy
drcat           Resource Data Resource Catalogue
chebi           Obo      Chemical Entities of Biological Interest
eco             Obo      Evidence code ontology
edam            Obo      EMBRACE Data and Methods ontology
edam_data       Obo      EMBRACE Data and Methods ontology (data)
edam_format     Obo      EMBRACE Data and Methods ontology (formats)
edam_identifier Obo      EMBRACE Data and Methods ontology (identifiers)
edam_operation  Obo      EMBRACE Data and Methods ontology (operations)
edam_topic      Obo      EMBRACE Data and Methods ontology (topics)
go              Obo      Gene Ontology
go_component    Obo      Gene Ontology (cellular components)
go_function     Obo      Gene Ontology (molecular functions)
go_process      Obo      Gene Ontology (biological processes)
pw              Obo      Pathways ontology
ro              Obo      Relations ontology
so              Obo      Sequence ontology
swo             Obo      Software ontology

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.open-bio.org/pipermail/emboss/attachments/20141204/0b01046d/attachment.html>