Sequence Fetcher

Jalview can retrieve sequences from certain databases using either the DBFetch service provided by the EMBL European Bioinformatics Institute, or, since Jalview 2.4, DAS servers capable of the sequence command (configured in DAS settings).

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 compiles the list of available sequence datasources from the currently defined DAS server registry.

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.
If you have DAS sources enabled, then you may have several sources for the same type of sequence identifier, and these will be grouped together in a sub-branch branch labeled with the identifier.

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.

Only retrieving part of a sequence

When using DAS sources (indicated by a "(DAS)"), you can append a range in addition to a sequence ID. For example, to retrieve 50 residues starting at position 35 in UNIPROT sequence P73137 using the UNIPROT DAS server, you would enter "'P73137:35,84'.
Full support for DAS range queries was introduced in Jalview 2.8

If you use the WSDBFetch sequence fetcher services (EMBL, UniProt, PFAM, and RFAM) in work for publication, please cite:

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)