The Use of Context-Sensitive Grammar For Modeling RNA Pseudoknots

In this study, a context-sensitive grammar is suggested to model various forms of RNA secondary structures, especially pseudoknots. Comparing with a conventional context-free grammar used to model secondary structures of RNA sequences, the use of context-sensitive grammar gives us an advantage of more natural representation of pseudoknots. The suggested grammar directly reflects the appearance characteristic of each form of RNA secondary structure, i.e., hairpins, internal loops, double helixes, and bulge loops. An augmented transition network and the Java programming language are suggested to implement the suggested context-sensitive grammar.