Figure 6.

Demonstration of coarse-graining for RNA secondary structures. Genotypes (RNA sequences) map to secondary structure phenotypes represented as dot-bracket structures produced by ViennaRNA program [58]. The RNAshapes program [57] then progressively computes coarse-graining at different ‘levels

’, increasingly ignoring nesting of secondary structure topological features. In this figure, three example sequences of length L = 70 are shown to map to their dot-bracket phenotypes. A cartoon of a neutral set (not actual size) has been drawn for each phenotype; network properties like robustness can be calculated for each phenotype. At

a higher level of coarse-graining (here, Level 3), multiple dot-bracket phenotypes all map onto the same coarse-grained phenotype. Accordingly, the coarse-grained phenotype has a neutral set comprising the individual neutral sets of the original phenotypes. Note that in practice there are many more secondary structures beyond those shown that map to this same coarse-grained phenotype; the analysis above is schematic.