Table of Contents
Database definition for EMBOSS
Download all definitions (embossrc file)
"embossrc" file including all databases definitions is available from here.
Please download this file and save as "~/.embossrc" on your home directory.
Database definitions (Nucleotide)
EMBL
DB embl [ type: N format: embl method: url dbalias: EMBL fields: "sv des org key" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[EMBL-all:'%s']+-ascii+1" comment: "Database of nucleotide sequence in Europe." ]
GENBANK(nucleotide)
DB genbankn [
type: N
format: genbank
method: url
url: "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=nucleotide&rettype=gb&retmode=text&id=%s"
dbalias: GENBANKN
comment: "The NIH genetic sequence database, an annotated collection of all publicly
available DNA sequences."
]
RefSeq(nucleotide)
DB refseqn [ type: N format: genbank method: url dbalias: REFSEQN fields: "sv des org key" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[REFSEQGENREL:'%s']+-ascii+1" comment: "Database providing non-redundant curated data representing knowledge of known genes." ]
DDBJ
DB ddbj [ type: N format: genbank method: url dbalias: DDBJ fields: "sv des org key" url: "http://xml.nig.ac.jp/rest/Invoke?service=GetEntry&method=getDDBJEntry&accession=%s" comment: "Database of nucleotide sequence in Japan." ]
FANTOM2
DB fantom2 [ type: N format: fasta method: url dbalias: FANTOM2 fields: "des" url: "http://fantom2.gsc.riken.jp/db/annotate/seqview.cgi?type=cdnaseq&masterid=%s" comment: "Functional Annotation of the Mammalian Genome (FANTOM) 2" ]
FANTOM3
DB fantom3 [ type: N format: fasta method: url dbalias: FANTOM3 fields: "des" url: "http://fantom3.gsc.riken.jp/db/reference/content.cgi?category=dnaseq&masterid=%s" comment: "Functional Annotation of the Mammalian Genome (FANTOM) 3" ]
Database definitions (Protein)
UniProtKB
DB uniprotkb [
type: P
format: swiss
method: url
dbalias: UNIPROTKB
fields: "sv des org key"
url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[UNIPROT-all:'%s']+-vn+2+-ascii"
comment: "The central hub for the collection of functional information on proteins,
with accurate, consistent and rich annotation."
]
RefSeq(protein)
DB refseqp [ type: P format: genbank method: url dbalias: REFSEQP fields: "sv des org key" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[REFSEQP:'%s']+-ascii" comment: "Database of protein information from REFSEQ." ]
GenBank(protein)
DB genbankp [ type: P format: genbank method: url dbalias: GENBANKP url: "http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=protein&rettype=gb&retmode=text&id=%s" comment: "Database of protein information from GENBANK" ]
Swiss-Prot
DB swissprot [
type: P
format: swiss
method: url
dbalias: SWISSPROT
fields: "sv des org key"
url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[SWISSPROT-all:'%s']+-vn+2+-ascii"
comment: "Database of protein sequences produced collaboratively by the Swiss
Institute for Bioinformatics (SIB) and the European Bioinformatics
Institute (EBI)."
]
SWALL
DB swall [ type: P format: swiss method: url dbalias: SWALL fields: "sv des org key" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[SWALL-all:'%s']+-vn+2+-ascii" comment: "A combined database of Swiss-Prot, SPTREMBL and TREMBLNEW. Does not contain REMTREMBL." ] DB sw [ type: P format: swiss method: url dbalias: SW fields: "sv des org key" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[SWALL-all:'%s']+-vn+2+-ascii" comment: "A combined database of Swiss-Prot, SPTREMBL and TREMBLNEW. Does not contain REMTREMBL." ]
UniParc
DB uniparc [ type: P format: swiss method: url dbalias: UNIPARC fields: "sv des org key" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[UNIPARC:'%s']+-ascii+-view+UniParc2Flat" comment: "A comprehensive and non-redundant database that contains most of the publicly available protein sequences." ]
PIR
DB pir [ type: P format: pir method: url dbalias: PIR fields: "sv des org key" url: "http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-e+[PIR:'%s']+-ascii" comment: "Protein Identification Resource." ]