Figure 16

Fold-alignment dotplot of U2 splicing factors (see Figure 13 for key). From a range of potential stems (faint red diagonal lines, plots a-b), the Pair SCFG resolves the true stems sharply using the comparative signal (white diagonal lines, plots d-e). The primary sequence alignment is highly uncertain (blurred red lines, plot c) but this uncertainty, including the deletion of a whole stem, is resolved by including structural information (broken diagonal line, plot f).