View→Sequence Features
When this option is selected, sequence features extracted from the Uniprot record for each sequence are displayed on the alignment.
Currently, sequence features are rendered in red or blue, dependent upon their type:
More information about the feature is given in a tooltip, which is viewed by moving the mouse pointer over a sequence feature. The description associated with the feature will then be displayed in a small label near the pointer.
After the Sequence Features option is selected, there may be some delay before the features are actually rendered, as jalview first determines if the sequences are contained in Uniprot and then retrieves any sequence records. This delay will normally only happen once for a particular set of sequences, as jalview caches uniprot records in a file in your home directory called '.jalview.uniprot.xml'.
The Sequence Identification Process
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In some cases, the ID used to retrieve Uniprot records may be out of date and you will be notified of that a 100% match between the sequence and a Uniprot record was identified, but the sequence name must be manually changed (by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.