Sequence Fetcher

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

The Sequence Fetcher dialog box 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. Please note, there will 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.

First, select the database you want to retrieve sequences from. Then, 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.

Fetching Individual PDB Chains
If you are retrieving sequences from the PDB, you can retrieve specific chains by appending a colon and the chain id to the PDB id. For example :

     1GAQ:A

Retrieving parts of large sequence records
When retrieving from DAS sequence sources, coordinate range arguments can be passed to the server using the standard DAS sequence command format:

      <AccessionId>:<start>,<end>

If you know a source understands this type of query format, then you should untick the checkbox for 'replace commas with semi-colons' so the range query can be passed to the server; otherwise, the query will be split into two (e.g 'Mito:1' and '85779' rather than 'Mito:1,85779'). In most cases, however, a source that supports range queries will include a range qualification in its example query, and Jalview will then automatically disable the 'replace commas with semi-colons' option.
The option to disable the comma to semi-colon translation was added in Jalview 2.6

If you use the WSDBFetch sequence fetcher services (EMBL, Uniprot, PDB and PFAM) 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)