FIGURE 1.

(A) Example secondary structure, (B) properties of its helices, and the resulting hishapes. hl, bl, il, and ml refer to hairpin, bulge, internal loop, and multiple loop, respectively. The letters m, b, and i appended to helix indices within hishapes indicate the loop type (multiple, bulge, and internal loop, respectively). Helix indices without suffix represent hairpin loops. Pairs of brackets in a hishape provide nesting information within multiloops. The structure plot in A was created using VARNA (Darty et al. 2009).