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-In some cases, the ID used to retrieve Uniprot records may be out of date - and you will be notified of that a 100% match between the sequence and a Uniprot - record was identified, but the sequence name must be manually changed (by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. -
-
-
- - + + +
+DAS Sequence Feature Retrieval
+Jalview includes a client for retrieving sequence features via +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, 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. +
+
DAS support was introduced in Jalview Version 2.1.
++ +