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Fig. 6 | BMC Bioinformatics

Fig. 6

From: RNAdualPF: software to compute the dual partition function with sample applications in molecular evolution theory

Fig. 6

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 sampled 2000 sequences without any subsequent filtering step. 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

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