Hierarchical analysis of RNA secondary structures with pseudoknots based on sections
Fig 5
Analysis of pseudoknot formation likelihood based on energetic predictions.
a) Connecting probability as a function of MFE gain for tmRNA and RNase P RNA sequences, defined as the ratio of actually connected section pairs to all section pairs with a given MFE value. b) Representative example of a non-connecting section pair with substantial MFE gain (80 kcal/mol), illustrating how conformational entropy losses can outweigh local energy gains in long sections (∼104 and ∼48 nucleotides).