Recognition and Modeling of RNA Pseudoknots Using Context-Sensitive Pattern Matching

In this study, a context-sensitive pattern matching is suggested to recognize and 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 searching of a particular p seudoknot gives us an advantage of more natural representation of RNA structures. The suggested technique directly reflects the appearance characteristic of each form of RNA secondary structure, i.e., hairpins, internal loops, double helixes, and bulge loops. Java language are used in this study to provide the user-interface, and also to implement the suggested context-sensitive searching of a specific pseudoknot