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embossrc [2011/01/26 11:03]
cory
embossrc [2014/01/18 07:44]
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-========= 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|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" 
-  ] 
- 
-===== 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."​ 
-  ] 
embossrc.txt ยท Last modified: 2014/01/18 07:44 (external edit)