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. 2011 Jun 14;27(13):i85–i93. doi: 10.1093/bioinformatics/btr215

Fig. 4.

Fig. 4.

A schematic diagram of the iterative refinement algorithm for the base-pairing probability matrix. A constraint on secondary structure for each level is denoted by a variant of the dot-parenthesis format: a matching parenthesis ‘()’ denotes an allowed base pair, a character ‘x’ indicates an unpaired base, and a dot ‘.’ is used for an unconstrained base.