If a sequence contains annotations, the Annotations and Tracks tab to the right of the sequence viewer will show a yellow arrow , and all the annotation types present on the sequence will be listed in this panel (see ﬁgure 8.2 ). Annotations that are directly on the sequence are listed ﬁrst, followed by annotations on tracks. Tracks with only one annotation type will show a single listing, whilst tracks with multiple annotations will show a list of the annotation types.
Individual annotation types can be turned on or oﬀ using the checkboxes to the left of the annotation type, or all annotations can be turned oﬀ by unchecking Show Annotations at the top of the panel. Note that turning an annotation type oﬀ does not remove it from the sequence, it only hides it from view.
Directly beneath the Show Annotations box is a ﬁlter text ﬁeld. Typing a term in this ﬁeld will highlight any annotations that contain the entered text in their name or qualiﬁers. To ﬁlter for a term in a speciﬁc ﬁeld, click the down arrow to the right of the box and choose the ﬁeld and term you wish to search for.
To quickly ﬁnd and move between instances of a particular annotation type on a sequence, click the small left/right buttons to the right of each annotation type. This will move the selection in the sequence view to the next or previous instance of that annotation type. This is useful for navigating large genomes or assemblies.
To customize the way an annotation type is displayed, click on the preview of the annotation arrow in the Annotation and Tracks window. This will bring up a popup menu containing the following options:
The popup menu for individual tracks has an additional option Color by / Heatmap. This will color annotations on that track according to the contents of a qualiﬁer ﬁeld, enabling the creation of annotation heatmaps by using a score value (or some other metric) stored in the qualiﬁer of an annotation.
The way annotations are drawn on the sequence can be further customized in the Advanced tab of the sequence viewer (see section 5.2.8 ).