Sequence Fetcher

Jalview can retrieve sequences from a range of sequence, 3D structure, genomic and domain family databases provided by EMBL-EBI.

The Sequence Fetcher can be opened via the "File" menu on the main desktop in order to retrieve sequences as a new alignment, or opened via the "File" menu of an existing alignment to import additional sequences. There may be a short delay when the sequence fetcher is first opened, whilst Jalview contacts each database's web API.

Every time a new fetcher is opened, you will need to select the database you want to retrieve sequences from the database chooser.

The databases are shown as a tree, and ordered alphabetically; tooltips are shown if you mouse over some sources, explaining what the database will retrieve. You can select one by using the up/down arrow keys and hitting return, or by double clicking with the mouse.

Once you have selected a sequence database, its fetcher dialog will open. Jalview provides two types of dialog:

1. The Free-text Search Interface
   Free-text search clients are provided for PDB (Since 2.9), and UniProt (Since 2.10). They provide access to each database's own query system, enabling you to retrieve data by accession, free text description, or any other type of supported field. For full details, see each client's help page:
   • PDB Sequence Fetcher
   • UniProt Sequence Fetcher
2. Accession based sequence retrieval
   
   To retrieve sequences, simply enter one or more accession ids (as a semi-colon separated list), or press the "Example" button to paste the example accession for the currently selected database into the retrieval box. Finally, press "OK" to initiate the retrieval.
   For the PDB and UniProt sequence fetchers, choose the "Retrieve IDs" tab to search for accession ids.

If you use the Sequence Fetcher, please remember to cite the corresponding services (linked to below):

• Ensembl - The Ensembl REST API
• EMBL/EMBLCDS - Provided by the European Nucleotide Archive's ENA Data API
  Note: Versions of Jalview prior to 2.11.1.1 employed the XML endpoint of the ENA browser, which was retired in August 2020.
• Uniprot - Free Text Search and Retrieval via the Uniprot REST API
• PDB - Free Text Search via the PDBe REST API and retrieval via WSDbFetch
  Pillai S., Silventoinen V., Kallio K., Senger M., Sobhany S., Tate J., Velankar S., Golovin A., Henrick K., Rice P., Stoehr P., Lopez R.
  SOAP-based services provided by the European Bioinformatics Institute.
  Nucleic Acids Res. 33(1):W25-W28 (2005)
  
  
• RFAM - a database of RNA families
• PFAM - a database of protein families
  Data is provided by the Interpro Web API