DAS Features

DAS Sequence Feature Retrieval

Jalview includes a client for retrieving sequence features via the Distributed Annotation System.

Open the Feature Settings panel by selecting "View -> Feature Settings..."
Click on the "DAS Settings" tabbed pane.
Select the sources to use for DAS feature retireval, then click the "Fetch DAS Features" button.
- Cancelling Feature Retrieval
  Press the Cancel Fetch button to immediately stop feature retrieval. This will not remove any features already added to the alignment, but will halt any outstanding DAS requests.The cancel fetch button is of particular use when one or more DAS annotation servers are not responding!

If your DAS source selection contains sources which use Uniprot accession ids, you will be asked whether Jalview should find Uniprot Accession ids for the given sequence names. It is important to realise that many DAS sources only use Uniprot accession ids, rather than Swissprot/Uniprot sequence names.

The Sequence Identification Process

The method of Uniprot accession id discovery is the same method which earlier Jalview versions used for sequence feature retrieval, and is now also used for PDB ID discovery . Essentially, Jalview will try to retrieve Uniprot records via the EBI's WSDbFetch interface using each sequence's ID string (or each string in the ID separated by the '∣' symbol).

If a uniprot record (or set of records) is found for a sequence, then the sequence is aligned to the one in the Uniprot record to determine the correct start and end residue positions (which are displayed when the 'Show Full Sequence ID' option is set).

If the alignment reveals differences between the sequence in the alignment and the one in the record, then Jalview will assume that the aligned sequence is not the one in the uniprot record.

In some cases, the ID used to retrieve Uniprot records may be out of date and a dialog box will be opened indicating that a 100% match between the sequence and a Uniprot record was identified, but the sequence name is different. In this case, the ID must be manually changed (by right clicking on the sequence ID and selecting Sequence→Edit Name), before Jalview will show its sequence features.

Note
Please remember to save your alignment if either the start/end numbering, or the sequence IDs were updated during the Uniprot ID retrieval process.

DAS support was introduced in Jalview Version 2.1.