View Annotations in sequence views

Figure 12.8 shows an annotation displayed on a sequence.

Image viewsequenceannotation
Figure 12.8: An annotation showing a coding region on a genomic dna sequence.

The various sequence views listed in Viewing annotations have different default settings for showing annotations. However, they all have two groups in the Side Panel in common:

The two groups are shown in figure 12.9.

Image annotationlayoutandtypes
Figure 12.9: The annotation layout in the Side Panel. The annotation types can be shown by clicking on the "Annotation types" tab.

In the Annotation layout group, you can specify how the annotations should be displayed (notice that there are some minor differences between the different sequence views):

In the Annotation types group, you can choose which kinds of annotations that should be displayed. This group lists all the types of annotations that are attached to the sequence(s) in the view. For sequences with many annotations, it can be easier to get an overview if you deselect the annotation types that are not relevant.

Unchecking the checkboxes in the Annotation layout will not remove this type of annotations them from the sequence - it will just hide them from the view.

Besides selecting which types of annotations that should be displayed, the Annotation types group is also used to change the color of the annotations on the sequence. Click the colored square next to the relevant annotation type to change the color.

This will display a dialog with five tabs: Swatches, HSB, HSI, RGB, and CMYK. They represent five different ways of specifying colors. Apply your settings and click OK. When you click OK, the color settings cannot be reset. The Reset function only works for changes made before pressing OK.

Furthermore, the Annotation types can be used to easily browse the annotations by clicking the small button (Image annotations_popup) next to the type. This will display a list of the annotations of that type (see figure 12.10).

Image annotationtypespopup
Figure 12.10: Browsing the gene annotations on a sequence.

Clicking an annotation in the list will select this region on the sequence. In this way, you can quickly find a specific annotation on a long sequence.

Note: A waved end on an annotation (figure 12.11) means that the annotation is torn, i.e., it extends beyond the sequence displayed. An annotation can be torn when a new, smaller sequence has been created from a larger sequence. A common example of this situation is when you select a section of a stand-alone sequence and open it in a new view. If there are annotations present within this selected region that extend beyond the selection, then the selected sequence shown in the new view will exhibit these torn annotations.

Image tornannotation
Figure 12.11: Example of a torn annotation on a sequence.