embossrc

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."
  ]