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SimulFold: Simultaneously Inferring RNA Structures Including Pseudoknots, Alignments, and Trees Using a Bayesian MCMC Framework

Figure 4

RNA Structure with Pseudoknot Predicted by SimulFold for the HDV Sequence of Organism AJ309880 Using the MCMC Results Generated with Parallel Tempering

The pairing probabilities estimated by SimulFold are colour-coded and range from bright green (high probability) to bright red (low probability). The pairing probabilities for this structure range from 0.62 for the pair at sequence positions {4, 38} to one for most of the base-pairs, e.g., the one at sequence positions {6, 36}. For this figure, we have adopted a nonlinear colouring scheme; otherwise, all base-pairs would simply come in slightly different shades of green.

Figure 4