DAS Sequence Feature Retrieval
Jalview 2.1 can be set up to retrieve sequence features using the Distributed Annotation System
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, not names of sequences.
The method of Uniprot accession id discovery is the same method which earlier
Jalview versions used for sequence feature retrieval, ie WSDbFetch provided
by the EBI.
The process is as described:
The Sequence Identification Process
Jalview will attempt to retrieve sequence features from Uniprot files using the EBI dbFetch web service using the given sequence names (or Uniprot ID, if available). A 100% match with the Uniprot record is required for Uniprot features to be view on a sequence.
The first step in the procedure for matching uniprot IDs to sequences is to use the ID (name) of each sequence to retrieve Uniprot records directly.
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In some cases, the ID used to retrieve Uniprot records may be out of date and you will be notified of that a 100% match between the sequence and a Uniprot record was identified, but the sequence name must be manually changed (by right clicking on the sequence ID and selecting Sequence→Edit Name), before Jalview will show its sequence features.