Sequence Features

Jalview can colour parts of a sequence based on the presence of sequence features - which may be retrieved from database records (such as Uniprot), the result of sequence motif searches or simply read from a sequence features file. You can also create features from the results of searches or the current selection, and edit features by double clicking on them.

Sequence Feature Colouring Styles

By default, Jalview will assign a color to each feature based on its type. These colours can be changed from the feature settings and amend features dialog boxes. Since Jalview 2.5, it is also possible to define feature colourschemes to shade features based on their associated scores or text labels.

Sequence Feature Groups

Since Jalview 2.08, sequence features assigned to a sequence can be organised into groups, which may indicate that the features were all retrieved from the same database (such as Uniprot features), or generated by the same analysis process (as might be specified in a sequence features file).

Sequence Feature Inheritance

Since Jalview 2.08, sequence features are global to a set of sequences appearing (independently or together) in many different alignments. Practically, this means features loaded onto one alignment can be viewed in any alignments involving the same sequences. The same sequence appears in different alignments when a new alignment is generated by submitting an existing set of sequences to one of the alignment or prediction web services, and when sequences are copied and pasted into other alignment windows.

View→Show Sequence Features

Toggle the display of sequence features in this alignment. If feature retrieval has not already been carried out, then Jalview will automatically try to fetch sequence features (as described below).

View→Sequence Feature Settings...

Once sequence features have been loaded, their display can be fully controlled using the alignment window's Sequence Feature Settings dialog box. Feature colour schemes and display parameters are unique to a particular alignment, so it is possible to colour the same sequence features differently in different alignment views.
Since Jalview 2.1, it is possible to add DAS features to an alignment via the DAS tabbed pane of the feature settings window.

View→Sequence ID Tooltip→Show Non-Positional features
Only available in application

Toggles the display of non-positional features in the sequence ID tooltip, and whether they will be included when sequence features are exported using "File→Export Features".

Precalculated Sequence Features may be added to an alignment from the command line, drag and drop, or from the "File→Load Features / Annotations" menu item. See the Features File Format for more details.