Fig. 8
For each of the 250 C. elegans precursor microRNAs from miRBase 20 and for each of the following cases (a), indicated in black, and (b), indicated in red, RNAdualPF generated 500 sequences, whose minimum free energy structure was identical to that of the corresponding wild type pre-miRNA (obtained by repeatedly generating samples with RNAdualPF until 500 sequences were found that folded exactly into the target structure). Case (a) - black lines: All RNAdualPF sequences have GC-content exactly equal to that of the Rfam sequence (Exact GC). Case (b) - red lines: RNAdualPF was used in default mode, without controlling GC-content (No GC). Case (c) - blue lines: wild type (WT) C. elegans data. Density plots are shown for (1) the expected base pair distance to target structure s 0 [9], (2) the ensemble defect to target structure s 0 [20], (3) the positional entropy [22], (4) Vienna structural diversity (called ensemble diversity in [14]), (5) Morgan-Higgs diversity [23], (6) expected proportion of native contacts (called ensemble neutrality in [21]). All measures were normalized by sequence length