Dynamic motifs

In the Side Panel of sequence views, there is a group called Motifs (see figure 14.22).

Image dynamicmotifs1
Figure 14.22: Dynamic motifs in the Side Panel.

The Workbench will look for the listed motifs in the sequence that is open and by clicking the check box next to the motif it will be shown in the view as illustrated in figure 14.23.

Image dynamicmotifs2
Figure 14.23: Showing dynamic motifs on the sequence.

This case shows the CMV promoter primer sequence which is one of the pre-defined motifs in CLC Genomics Workbench. The motif is per default shown as a faded arrow with no text. The direction of the arrow indicates the strand of the motif.

Placing the mouse cursor on the arrow will display additional information about the motif as illustrated in figure 14.24.

Image dynamicmotifs3
Figure 14.24: Showing dynamic motifs on the sequence.

To add Labels to the motif, select the Flag or Stacked option. They will put the name of the motif as a flag above the sequence. The stacked option will stack the labels when there is more than one motif so that all labels are shown.

Below the labels option there are two options for controlling the way the sequence should be searched for motifs:

The list of motifs shown in figure 14.22 is a pre-defined list that is included with the CLC Genomics Workbench. You can define your own set of motifs to use instead. In order to do this, you first need to create a motif list (Image motiflist) and then click the Manage Motifs button. This will bring up the dialog shown in figure 14.25.

Image dynamicmotifs4
Figure 14.25: Managing the motifs to be shown.

At the top, select a motif list by clicking the Browse (Image browse) button. When the motif list is selected, its motifs are listed in the panel in the left-hand side of the dialog. The right-hand side panel contains the motifs that will be listed in the Side Panel when you click Finish.