RNA structure prediction using positive and negative evolutionary information
Fig 2
RNA models used by the CaCoFold algorithm.
(a) The Nussinov grammar implemented by the maxCov algorithm uses the R-scape E-values of the significantly covarying pairs, and maximizes the sum of -log(E-value). (b) The RBG model used by the first layer of the folding algorithm. (c) The G6X model used by the rest of the layers completing the non-nested part of the RNA structure. For the RBG and G6X models, the F nonterminal is a shorthand for 16 different non-terminals that represent stacked basepairs. The three models are unambiguous, that is, given any nested structure, there is always one possible and unique way in which the structure can be formulated by following the rules of the grammar.