Abstract
Much attention has been paid to RNA secondary structure predicition based on context-free grammar (cfg) since cfg can represent stem-loop structure by its derivation tree. Especially, techniques based on CKY (Cocke-Kasami-Younger) algorithm have been widely investigated [1]. Pseudoknots play an important role in RNA functions such as ribosomal frameshifting and splicing. A database (PseudoBase) for RNA pseudoknots has been constructed [9]. Unfortunately, it is known that cfg cannot represent pseudoknot structure and a few grammars have been proposed to represent pseudoknots [5, 8]. However, the relation among the expressive (generative) power of these grammars and/or other grammars in formal language theory beyond cfg has not been clarified. The authors have proposed a class of grammars called multiple context-free grammars [3, 7]. In this research, we identify grammars for RNA secondary structure [5, 8] as subclasses of mcfg and also clarify the inclusion relation among the class of languages generated by these grammars.
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