Visualisation of Sequence Features

Jalview can visualize sequence features - the positional annotation present on parts of a sequence, as colours overlaid on corresponding positions in the alignment. Features may be coloured either according to their type, or for a particular type, according to each feature's associated label, score, or other attributes.

The Feature Settings dialog box controls the order and display of each feature type, and also allows filters and colour schemes to be configured.

Feature Display Settings dialog for 'sequence_variant' features imported from VCF

The Feature Display Settings has the following controls:

Colour

- Simple Colour - select this to assign a given colour to any features of this type. The assigned colour can be changed by clicking on the colour box.
- Colour by text - this option derives a colour for each feature based on its label, or any other attributes presented via the drop-down menu.
- Graduated Colour - shade features according to associated score, or other numeric attribute.
  - Min and Max Color boxes - Click on these boxes to set the minimum and maximum colours for the shading scheme.
  - Threshold type combo box - Specify an exclusion threshold.
    Set the threshold using the slider or type it in to the text box. The threshold cannot be set outside the available range of values observed for the selected attribute.
  - Threshold is Min/Max - When checked, the threshold will be used as the upper or lower limit for shading using the Min and Max colour.

Filters
Any number of filter conditions may be specified to select features based on one or more attributes. The join condition specifies whether all filters must apply (And) or whether any one filter must apply (Or) for a feature to be selected.

The filters available depend on the type of attribute:

- Numeric - specify a threshold above, equal to or below which a feature will be selected or ignored.
- String - select or ignore features based on presence, absence, equivalence, or containment of a string (not case sensitive).

The filters and colour schemes active for a particular feature type are shown in the Colour and Configuration columns in the feature settings dialog. Styles and filters can be saved as a Jalview Feature Colours file, and are also exported and imported via Jalview Feature files.

Icon styles for feature rendering styles

When a graduated colour scheme is applied to a feature according to the value of a particular attribute, it is indicated in the feature settings or amend feature dialog box by the following types of icon:

Type of Colouring | Icon
Graduated colour by Feature Score |
Graduated colour thresholded (less than) by feature Score (or other attribute) |
Graduated colour thresholded (greater than) by feature Score (or other attribute) |
Colour by Feature Label |
The current threshold and attribute is shown in the icon's tooltip.

Graduated feature colours were introduced in Jalview 2.5. Attribute based colouring and filters were added in Jalview 2.11.