+
+ 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 its 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 identification 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++ In some cases, the ID used to retrieve records may be out of date and + a dialog box will be opened indicating that a 100% match between the + sequence and the record was identified, but the sequence name is + different.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). +