Fig. 2.

Representative ShapeKnots structure prediction for the SAM I riboswitch. Base pair predictions are illustrated with colored lines: green, correctly predicted; red, missed base pair relative to the accepted (29) structure; and purple, prediction of a pair not in the accepted structure. (Left) Predictions without SHAPE data. (Center and Right) Predictions made when SHAPE data were included, using circle plot and conventional representations, respectively. Sensitivity (sens) and ppv are listed for each structure. SHAPE data are shown as colored nucleotide letters on a black, yellow, and red scale for low, medium, and high SHAPE reactivities, respectively. Plots were generated using the CircleCompare program in the RNAstructure package.