+
Discovering Database References for Sequences
+Database references are associated with a sequence are displayed as a
+list in the tooltip shown when mousing over its sequence ID. Jalview
+uses references for the retrieval of PDB structures and DAS features, and for
+retrieving sequence cross-references such as the protein products of a
+DNA sequence.
Initiating reference retrieval
+The application provides three ways to access the retrieval function. Either:
+
Jalview discovers references for a sequence by generating a set +of ID queries from the ID string of each sequence in the alignment. It +then tries to query a subset of all the databases it can access in order to match +the alignment sequence to any records retrieved from the database. If a +match is found, then the sequence is annotated with that database's +reference, and any cross-references that it's records contain.
+The Sequence Identification Process
+The method of accession id discovery is derived from the method which
+earlier Jalview versions used for Uniprot sequence feature retrieval,
+and was originally restricted to the identifaction of valid Uniprot
+accessions.
+Essentially, Jalview will try to retrieve records from a subset of the databases
+accessible by the sequence
+fetcher using each sequence's ID string (or each string in the ID
+separated by the '∣' symbol).
If a record (or set of records) is retrieved by any query derived +from the ID string of a sequence, then the sequence is aligned to the +ones retrieved to determine the correct start and end residue positions +(which are displayed when the 'Show Full Sequence ID' option). This is +important for the correct display of the location of any features +associated with that database.
+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 retrieved record.
+In some cases, the ID used to retrieve records may be out +of date and a dialog box will be opened indicating that a 100% match +between the sequence and the record was identified, but the +sequence name is different. In this case, the can be manually +changed (by right clicking on the sequence ID and selecting Sequence→Edit +Name). +