EBI Dbfetch

Database	Search Items	Format	Style
EMBL EMBLCON EMBLANN EMBLCDS EMBLSVA Ensembl Gene Ensembl Transcript UniProtKB UniSave UniRef100 UniRef90 UniRef50 UniParc IPI RefSeq InterPro PDB HGVbase GenomeReviews EPO Proteins JPO Proteins KIPO Proteins USPO Proteins Medline		default embl fasta emblxml insdxml	default html raw

Upload File	Format	Style
	default fasta embl emblxml insdxml uniprot swissprot	default html raw

Dbfetch Help

• From the browser
  
  Follow these instructions...
  
  
  1. Selecting a database:
     -If you are using the first form to paste your search items: choose a database name from this form...more
     -If you are using the second form to upload your search items: the database name will be included at the beginning of each line line of the upload file followed by a colon...more
     
     
  2. Entering your search terms:
     These MUST BE in the appropriate database format, up to 200 search items can be queried in one run.
     -If you are using the first form: seperate search items with a comma or space...more
     -If you are using the second form: seperate search items with a new line...more
     
     
  3. Choosing an output format:
     Here you can choose the simpler fasta format, or the databases' default format for the chosen database...more
     
     
  4. Style:
     You can get your results as text, ot html...more
     
     
  5. Retrieve!
     You are now ready to fetch your results, by pressing the Retrieve button.
     
     
  Search Items
  
  You may enter up to 200 search items for your chosen database.
  
  Multiple search terms should be sepatated by EITHER a space OR a comma.
  
  e.g. EMBL
  
  "AE014292,AE017197,AE017354 " or "AE014292 AE017197 AE017354"
  
  e.g. UniProtKB
  
  "1433X_MAIZE,1433T_RAT,ACR2_YEAST" or "1433X_MAIZE 1433T_RAT ACR2_YEAST"
  
  Upload File
  
  Here you may upload a file in the specified format.
  
  You may retrieve up to 200 entries.
  
  Entries in the uploaded file all need to belong to the same database.
  
  Each entry you wish to retrieve MUST be on a new line and in the format: "database name":"id"
  
  e.g. EMBL
  

       embl:AE014292
       embl:AE017197
       embl:AE017354

  
  e.g. UniProtKB
  

       uniprotkb:A1AG1_HUMAN
       uniprotkb:A1AT_PIG
       uniprotkb:ACR2_YEAST

  
  Supported Databases and Database ID Format
  
  Currently supported databases include EMBL, UniProtKB, PDB, Medline, RefSeq, HVGBase, EMBLSVA, UniRef100, UniRef90, UniRef50 and UniParc.
  
  
  • The EMBL Nucleotide Sequence Database (EMBL) entries can be retrieved either by accession number (e.g. M10051) or by entry name (e.g. HSINSR).
    
    
  • EMBL Sequence Version Archive (SVA) entries can be retrieved by accession number (e.g. J00231) or by sequence version e.g. J00231.1).
    
    
  • EMBLCDS entries can be retrieved by entry name (e.g. AAA59452).
    
    
  • Ensembl Gene entries can be retrieved by entry name (e.g. ENSG00000139618).
    
    
  • Ensembl Transcript entries can be retrieved by entry name (e.g. ENST00000359752).
    
    
  • UniProtKB entries can be retrieved by entry name (e.g. INSR_HUMAN) or by accession number (e.g. P06213).
    
    
  • UniProt Archive (UniParc) entries can be retrieved by accession number (e.g. UPI0000046364, UPI00001B3DCE).
    
    
  • UniRef100, UniRef90 and UniRef50 entries can be retrieved by accession number ( UniRef100_P06213 for UniRef100, UniRef90_P06213 for UniRef90 and UniRef50_P06213 for UniRef50 ).
    
    
  • Other search examples

    MEDLINE: 2859121
    IPI: IPI00025803, IPI00220325
    HGVBASE: SNP000000106,
    SNP000000107, SNP000002179, SNP000002180, SNP000005123, SNP000018488
    InterPro: IPR006212, IPR008266, IPR008957, IPR009030, IPR011009
    PDB: 1GAG, 1I44, 1IR3, 1IRK, 1P14, 1RQQ
    

    
    
    
  Output Format
  
  The sequence/database format of the results. Sequence formats are simply the way in which the amino acid or DNA sequence is recorded in a computer file. Different programs expect different formats, so if you are to submit a job successfully, it is important to understand what the various formats look like. To learm more about sequence formats, please see the 2Can Support Portal at http://www.ebi.ac.uk/2can/tutorials/formats.html
  
  The default is often the default format for the specified database, which can also can be selected in the drop down list.
  
  e.g. The default for the UniProt Database is SWISS format.
  
  See an example of this format at http://www.ebi.ac.uk/2can/tutorials/formats.html#swiss
  
  Fasta format contains a one line header followed by lines of sequence data. Sequences in fasta formatted files are preceded by a line starting with a " >" symbol. The first word on this line is the name of the sequence. The rest of the line is a description of the sequence.
  
  e.g.
  
  

  >uniprot|P13346|FOSB_MOUSE Protein fosB. 
  MFQAFPGDYDSGSRCSSSPSAESQY

  Learn more about this format at http://www.ebi.ac.uk/2can/tutorials/formats.html#fasta
  
  If no format is specified, as in an http request, the default format will be used.
  
  EMBL XML formats , there are two XML formats availabe from the EMBL database.
  EMBLXML : XML format for the EMBL nucleotide sequence database , developed internally.
  INSDXML : XML format for EMBL the nucleotide sequence database, developed in collaboration with NCBI(genbank) and DDBJ.
  DTD for INSDXML and the DTD/XML Schema for EBMLXML can be found here.
  
  Style
  
  The results can either be delivered as raw text or as html, specify here which style you prefer.
  
  The default style is html.
  
  
• from within a script - examples of the url for all styles and formats
  
  

  For people interested in programmatic access to the Dbfetch functionality, we recommend using our new Web Services version of Dbfetch: WSDbfetch.
  
  Alternatively, you can use dbfetch for direct access:
  
  Making scripted http requests to dbfetch is very simple, the parameters which can be used are db, id, format and style. Of these parameters only db and id are required fields. When omitting to use format and/or style, the defaults for the chosen database will be used (the default style is always html).
  
  The URL to dbfetch is always of this format:
  http://www.ebi.ac.uk/cgi-bin/dbfetch?db=DB_NAME&id=IDS&format=FORMAT_NAME&style=STYLE_NAME
  
  

  • DB_NAME - Must be chosen from the table below
  • IDS - Single id/acc or comma/white-space separated list (id1 or id1 id2 id3 or id1,id2,id3)
  • FORMAT_NAME - Name of the output format, varies between databases
  • STYLE_NAME - Name of the output style, available styles are raw and html

  
  The available databases are:
  
  

  NAME	KEY(use this)
  EMBL	embl
  EMBLCON	emblcon
  EMBLCDS	emblcds
  EMBLSVA	emblsva
  UniProtKB	uniprotkb
  UniSave	unisave
  UniRef100	uniref100
  UniRef90	uniref90
  UniRef50	uniref50
  UniParc	uniparc
  IPI	ipi
  RefSeq	refseq
  InterPro	interpro
  PDB	pdb
  HGVbase	hgvbase
  GenomeReviews	genomereviews
  EPO Proteins	epo_prt
  JPO Proteins	jpo_prt
  KIPO Proteins	kipo_prt
  USPO Proteins	uspto_prt
  Medline	medline
  Ensembl Gene	ensemblgene
  Ensembl Transcript	ensembltranscript

  
  
  To find the available format and styles for the different databases, select the database in the search form and the format and style drop down will contain the available options.
  
  Examples:
  
  http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBL&id=J00231,HSFOS,ROD894,LOP242600
  
  Instead of the default raw (plain ASCII) style, entries can also be retireved in plain text (raw):
  http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBL&id=J00231,HSFOS,ROD894,LOP242600&style=raw
  
  It is also possible to retrieve Fasta formatted sequences:
  http://www.ebi.ac.uk/cgi-bin/dbfetch?db=EMBL&id=J00231,HSFOS,ROD894,LOP242600&format=fasta
  
  Because of backward compatibility issues the program can be simply called by giving one or more EMBL accession numbers or entry names:
  http://www.ebi.ac.uk/cgi-bin/dbfetch?J00231