Generation of RNA pseudoknots with controlled ambiguous grammar

A controlled ambiguous grammar has been suggested to generate more than one parse tree for the prediction of various RNA secondary structures of a given RNA sequence. More than one parse tree implies various formations of RNA pseudoknots for the same RNA sequence reflecting pH, temperature, etc. The use of controlled ambiguous grammar is a novel approach in that the ambiguity of a programming language grammar has been utilized, that should be avoided when making a practical programming language. In this study, a controlled ambiguity of context-free grammar corresponding to the value of pH parameter has been suggested to generate various configuration of RNA pseudokots.