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.
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