PhyloGibbs: A Gibbs Sampling Motif Finder That Incorporates Phylogeny
Figure 2
An Alignment of Four Sequences Showing Three Legitimate Windows and One Illegitimate Window
Vertically aligned capital letters are phylogenetically related bases, assumed to have evolved from a common ancestor. Thus, any window placed on these bases is extended to cover all related bases. Three legitimate windows are surrounded by solid boxes. The window surrounded by the dotted box is illegitimate because the gap in the top sequence makes the alignment of bases inconsistent. Note that lower case letters are not aligned and that, in order to complete a window with aligned sequences, one may slide lowercase bases “through” adjoining gaps. For example, if the window on the bottom two sequences were to move two steps to the left, the “c” and “a” on the left side of the preceding gaps would slide through the gaps to the right to complete the window.