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).

Web services can also add annotation to an alignment (see the JNet web service), 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.
• Show Values in Text Box
  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.

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.
• 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

In the current version of Jalview, reordering of the annotation rows is not possible. If you save your annotation as a Jalview file, however, it will be reloaded with user annotations at the top (nearest the alignment), above any of the automatically generated Conservation, Quality or consensus annotations. Finally, the Jalview GUI will not, as yet, allow you to output Jalview annotation files for the current alignment, change the line colour, display style, or create groups of quantitative annotation rows.