Hi Bruce,
the genbank is done via ncbi entrez.
With "showserver" you can see where the configuration file is located (default
is /usr/local/emboss/share/EMBOSS/server.entrez).
In this file you can see, which ncbi databases are configured and which fields
can be queried.
So to get a refseq you can use: "entret entrez:nucleotide:NM_....."
But for unknown reasons on my system it takes in the range of a minute before
the entry is returned. This issue can be related to our firewall.
Therefore I use for ncbi an alternative solution:
I have configured this database definition:
--------------------
DB ncbin [
type: N
format: genbank
method: app
app: "/usr/local/emboss/bin/ncbi_fetch nucleotide:%s"
comment: "NCBI GenBank Nucleotide" ]
---------------------
ncbi_fetch is a simple perl script using wget to call the ncbi eutils.
-------------------------------
#!/usr/local/bin/perl
# %s passed from emboss entret or seqret
$id=$ARGV[0];
$entry=`/usr/local/bin/wget --wait=3 --waitretry=3 -q --cache=off --timeout=10
-O -
"http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&id=$id&rettype=gb&retformat=text"`;
print $entry;
--------------------------------
Hope this helps.
Kind regards,
David.
Von: [email protected]
[mailto:[email protected]] Im Auftrag
von Citron, Bruce A.
Gesendet: 04 December 2014 20:07
An: [email protected]
Betreff: [EMBOSS] Remote Databases and possibly drcat
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
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