Alignment Annotation

In addition to the definition of groups and sequence features, Jalview can display symbols, line graphs, histograms and heatmaps under the columns of an alignment. These annotation tracks are displayed in the annotation area below the alignment. The annotation area's visibility is controlled with the View→Show Annotation option.

Types of annotation

Importing and exporting annotation
Annotations on an alignment view are saved in Jalview project files. You can also load Annotations Files in order to add any kind of quantitative and symbolic annotations to an alignment. To see an example, use the Export Features/Annotation option from an alignment window's File menu.

Layout and display controls
Individual and groups of annotation rows can be shown or hidden using the pop-up menu obtained by right-clicking the label. You can also reorder them by dragging the label to a new position with the left mouse button. The Annotations menu provides settings controlling the ordering and display of sequence, group and alignment associated annotation. The Colour by annotation option in the colour menu allows annotation to be used to shade the alignment. Annotations can also be used to select or hide columns via the dialog opened from the Selection menu. You can also colour, select or hide columns of the alignment using any displayed annotation row by right-clicking its label and selecting the option from the displayed pop-up menu.

Adjusting the height of histograms, line graphs and heatmaps
The height of line graphs, bar charts and predicted alignment error (PAE) matrix heatmaps can be adjusted simply by click-dragging them up or down to increase or decrease the height. Hold down SHIFT to adjust the height of all instances of a particular type of annotation row.

Sequence Highlighting and Selection from Annotation

A single click on the label of an annotation row associated with sequences and sequence groups will cause the associated sequences to be highlighted in the alignment view. Double clicking the label will select the associated sequences, replacing any existing selection. Like with other kinds of selection, shift double-click will add associated sequences, and Ctrl (Mac CMD) double-click will toggle inclusion of associated sequences in the selection.

Selecting, analysing and exploring heatmap annotation

Mouseovers on heap annotation tracks result in a tooltip displaying information about the range of values under the mouse, and their associated row and column in the heatmap.
For Predicted Alignment Error (PAE) matrices, the only form of heatmap annotation currently supported by Jalview, both the vertical and horizontal positions in the heatmap correspond to positions in linked 3D structures and the associated sequence in the alignment - so clicking any position in a heatmap will select columns in the alignment corresponding to the selected row(s) and column under the mouse.

Heatmap annotations can also be clustered, enabling columns of the alignment to be grouped based on similarity of the sets of values in the heatmap. Double clicking a region of a clustered heatmap annotation will select both the row and columns of the alignment grouped by the clustering. See clustering PAE matrices for more information.

Interactive Alignment Annotation

Annotation rows are added using the Annotation Label menu, which is obtained by clicking anywhere on the annotation row labels area (below the sequence ID area).

Editing labels and secondary structure annotation rows

Use the left mouse button to select a position along the row that are to be annotated - these regions will be coloured red. Press Control or shift in combination with the left-click to either select an additional position, or a range of positions on the alignment.

Once positions have been selected, use the right mouse button and select one of the following from the annotation menu:

User defined annotation is stored and retrieved using Jalview Archives.

Current Limitations

The Jalview user interface does not support interactive creation and editing of quantitative annotation (histograms and line graphs), or to create annotation associated with a specific sequence or group. It is also incapable of annotation grouping or changing the style of existing annotation (e.g. to change between line or bar charts, or to make multiple line graphs). These annotation capabilities are only possible by the import of an Annotation file.