Annotations (or tags) can be placed at any position on readings or on the consensus. They are usually used to record positions of primers for walking, or to mark sites, such as repeats or compressions, that have caused problems during sequencing. They can also be used to contain feature table data as read from an EMBL format sequence file (see section Reference sequences). Each annotation has a type such as "primer", a position, a length, a strand (forward, reverse or both) and an optional comment. Each type and strand has an associated colour that will be shown on the display. For information on searching for annotations see section Search by Tag Type, and section Search by Annotation Comments.
To create an annotation, make a selection and then select "Create Tag" from the contig editor commands menu. See section The Commands Menu. This will bring up a further window; the "tag editor" (shown above). The "Type:" button at the top of the editor invokes a selectable list from which tag types can be chosen. See below.
Use this to select the desired type of annotation.
Next the strand of the annotation can be selected. This will be displayed as one of "<----->", "<-----" and "----->". The comment (the box beneath the buttons) can be edited using the usual combination of keyboard input and arrow keys. The "Save" button will exit the tag editor and create the annotation. To abandon editing without creating the annotation use the "Cancel" button.
To edit an existing annotation, position the editing cursor within a annotation and select "Edit Tag" from the commands menu. Once again the tag editor will be invoked and operates as before. Here "Save" will save the edited changes and "Cancel" will abandon changes.
Removing a annotation involves positioning the editing cursor within an annotation and selecting "Delete Tag" from the commands menu.
As usual, "undo" can be used to undo any of these annotation creations, edits and removals.
The Control-Q key sequence may be used to toggle the displaying of tags. Pressing it once will prevent all tags from being displayed in the editor. This is sometimes useful to see any colouring information underneath the tag. Pressing Control-Q once more will redisplay them.