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

• Sequence associated annotation.
  Data displayed on sequence associated annotation rows are associated with the positions of a sequence. Often this is 'Reference annotation' such as secondary structure information derived from 3D structure data, or from the results of sequence based prediction of secondary structure and disorder. If reference annotations are available for a particular sequence or the current selections, they can be shown by selecting the Add Reference Annotation option in the sequence or selection popup menu.
  Jalview currently supports the following sources of sequence associated annotation:
  • Protein and RNA Secondary Structure
    These can be obtained from JPred and RNAAliFold secondary structure prediction services, and also for imported 3D Structure data.
  • Temperature factor, Model Quality or AlphaFold Reliability
    Jalview extracts and displays values from the 'Temperature Factor' column of PDB and mmCIF files, interpreted in various ways. For regular PDB files, these are imported directly as 'Temperature Factor', but for structures from computational methods such as EBI-AlphaFold, these values are interpreted and shown as 'AlphaFold Reliability' or 'Model Quality' according to the source.
  • Predicted Alignment Error heatmaps
    These are displayed for models retrieved from EBI-AlphaFold or when a supported JSON format PAE file is provided when importing a local 3D structure file.
• Group associated annotation.
  Data can be associated with groups defined on the alignment. If sequence groups are defined, Conservation and Consensus annotation can be enabled for each group from the Annotations menu, or can be imported from a Jalview Annotations file.
• Alignment associated annotation.
  Annotation rows associated with columns on the alignment are simply 'alignment annotation'. Controls allow you to interactively create alignment annotation to add labels and symbols to alignment columns. Jalview's consensus, conservation and quality calculations also create histogram and sequence logo annotations on the alignment.

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.

• Rows and columns in the heatmap corresponding to currently selected columns in the alignment are shown as red horizontal and vertical bands.
• Rectangular Selections can be created by pressing CMD (or Window/Meta key) whilst click-dragging across an area of the annotation.
• Data driven selections - e.g. selecting regions of low values of Predicted Alignment Error in a heatmap can be dome by pressing CTRL whilst clicking a region of an alignment.

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).

• Add New Row
  Adds a new, named annotation row (a dialog box will pop up for you to enter the label for the new row).
• Edit Label/Description
  This opens a dialog where you can change the name (displayed label), or the description (as shown on the label tooltip) of the clicked annotation.
• Hide This Row
  Hides the annotation row whose label was clicked in order to bring up the menu.
• Hide All <label>
  Hides all annotation rows whose label matches the one clicked. (This option is only shown for annotations that relate to individual sequences, not for whole alignment annotations. Since Jalview 2.8.2.)
• Delete This Row
  Deletes the annotation row whose label was clicked in order to bring up the menu.
• Show All Hidden Rows
  Shows all hidden annotation rows.
• Export Annotation (Application only)
  Annotations can be saved to file or output to a text window in either the Jalview annotations format or as a spreadsheet style set of comma separated values (CSV).
• Show Values in Text Box (applet only)
  Opens a text box with a list of comma-separated values corresponding to the annotation (numerical or otherwise) at each position in the row. This is useful to export alignment quality measurements for further analysis.
• Scale Label To Column(introduced in 2.5)
  Selecting this toggles whether column labels will be shrunk to fit within each column, or displayed using the view's standard font size.
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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:

• Helix
  Marks selected positions with a helix glyph (a red oval), and optional text label (see below). A dialog box will open for you to enter the text. Consecutive ovals will be rendered as an unbroken red line.
• Sheet
  Marks selected positions with a sheet glyph (a green arrow oriented from left to right), and optional text label (see below). A dialog box will open for you to enter the text. Consecutive arrows will be joined together to form a single green arrow.
• RNA Helix (only shown when working with nucleotide sequences)
  Marks selected positions as participating in a base pair either upstream or downstream. When the dialog box opens, enter a '(' to indicate these bases pair with columns upstream (to right), and ')' to indicate this region pairs with bases to the left of the highlighted columns. Other kinds of base-pair annotation are also supported (e.g. 'A' and 'a', or '<' and '>'), and Jalview will suggest an appropriate symbol based on the closest unmatched parenthesis to the left.
  If any brackets do not match up, then an orange square will highlight the first position where a bracket was found not to match.
• Label
  Set the text label at the selected positions. A dialog box will open for you to enter the text. If more than one consecutive position is marked with the same label, only the first position's label will be rendered.
• Colour
  Changes the colour of the annotation text label.
• Remove Annotation
  Blanks any annotation at the selected positions on the row. Note: This cannot be undone

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.