BayesFold allows you to enter up to nine motifs which can then be displayed on the structure drawing. As described in section Chapter 2, QuickStart Guide, displaying motifs on the drawing can be very helpful in determining whether the same regions of a sequence are brought together in multiple structures.

Motifs are entered in the motif textbox below the drawing (see above); when motifs have been entered or changed, the "Apply Motifs" button next to the motifs text box will become enabled. Clicking this button applies the motifs so that they can subsequently be colored by opening the formatting palette and selecting the "motifs" coloring for bases (see Section 3, “Understanding the Format Palette”). Note that applied motifs will be stored but NOT colored unless this formatting option is selected.

Multiple motifs should be separated by commas. Motifs may include degenerate bases, in which case all subsequences that could match the motif will be highlighted; hyphens may be used to represent gaps. There is no limit on the length of motifs. Motifs are assigned colors in the order they are entered in the motif list; at this time, the colors are not adjustable.

Since multiple motifs are allowed, they may sometimes overlap. In this case, bases will be colored by the last motif in the motif list that matched them. Thus, rearranging the order of the motif list can alter the display of the motifs; to make sure that a particular motif is always displayed on top of all others, place it last in the motif list.