Alignment Annotation
In addition to the definition of groups, Jalview also allows 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).
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
Annotation is stored and retrieved using Jalview Archives. Quantitative
annnotation is also possible, but currently only possible with the
JNet web service, or by creating your own Jalview Archive (which
contains XML conforming to the Jalview-Vamsas XML schema).
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.