DAS Sequence Feature Retrieval
-Jalview includes a client for retrieving sequence features via +
Jalview includes a client for retrieving sequences and their features via the Distributed Annotation System.
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. +The database reference +fetcher documentation describes how Jalview discovers what database +references are appropriate for the sequences in the alignment.