Alignment Annotation

In addition to the definition of groups and sequence features, Jalview can display symbols and graphs under the columns of an alignment, and allow you to mark particular columns of an alignment and add symbols and text in the annotation area shown below the alignment (which may be hidden if View→Show Annotation is not ticked). Any displayed annotation row can be hidden (using the pop-up menu obtained by right-clicking the label), or re-ordered by dragging the label to a new position with the left mouse button.

Web services can also add annotation to an alignment (see the JNet and Disorder protein structure prediction services), and as of Jalview 2.08 quantitative and symbolic annotations can be added to an alignment via an Annotations File dragged into the alignment window or loaded from the alignment's file menu.

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).
- Hide Row
  Hides the annotation row whose label was clicked in order to bring up the menu.
- Delete 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.

Editing Label and secondary structure Annotation

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

Once the desired position has been selected, use the right mouse button to open the annotation menu:

- Helix
  Mark 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
  Mark 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)
  Mark 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.
  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 that 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

As of version 2.5, the Jalview user interface does not support the creation and editing quantitative annotation (histograms and line graphs), or to create annotation associated with a specific sequence. It is also incapable of annotation grouping or changing the style of existing annotation (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.