RNA Secondary Structure Prediction Based on Formal Grammars

摘要

Recently, much attention has been paid to RNA secondary structure prediction that applies parsing techniques in formal grammars. Since base pairs in typical RNA sequences occur in a nested way, secondary structures have been successfully modeled by context-free grammars (CFGs). On the other hand, there are substructures called pseudoknots where some base pairs occur in a crossed fashion, and joint structures called kissing hairpin loops caused by RNA-RNA interactions, which cannot be represented by CFGs. This paper is dedicated to discussing several grammatical approaches to the prediction of RNA secondary structure including pseudoknots and kissing hairpin loops.