-
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:
-
+ Discovering Database References for Sequences
+ Database references associated with a sequence are displayed as an
+ abbreviated list in the tooltip shown when mousing over its sequence
+ ID, and can be viewed in full via the
+ Sequence Details window. .
+ Jalview also 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).
+ 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.
+ 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). + 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).