Visualization of RNA structure conservation in a sequence alignment. Comparison of RNA structure visualization using (A) MFOLD, (B) 3D, and (C) 2D contour plots produced by StructureDist of example RNA secondary structure elements (stem–loop, interrupted stem–loop, and clover leaf). Predicted consensus positions of terminal loops in RNAFold RNAsubopt output were aligned and plotting depths based on pairings either side calculated. They were depicted as canyons corresponding to duplex lengths (B) and then rotated to create a 2D representation of sequences in the alignment (x-axis) and alignment position (y-axis) and color-coded depth. (D) Application of contour plotting to an alignment of HCV sequences in the core/E1 region in three- and two-dimensional representations. Pairing predictions represent as majority role consensus derived from the ensemble of suboptimal folds produced by the RNAsubopt program; similar results are obtained irrespective of whether suboptimal folds are sampled from a defined range of MFE values from the optimum, suboptimal structures sampled based on their Boltzmann weights in a partition function, or Zuker suboptimals (Supplemental Fig. S2B; Supplemental Data).
