embossrc

Database definition for EMBOSS

Download all definitions (embossrc file)

"embossrc" file including all databases definitions is available from http://soap.g-language.org/kbws/embossrc.

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." ]