Modeling RNA Secondary Structures Using Tree Grammars

Abstract

This paper proposes a grammatical tool, called tree adjunct grammar with tag for RNA (denoted by TAG²_RNA), for representing secondary structures of RNAs, and shows some example TAG²_RNA grammars for fairly complicated RNA secondary structures. We then demonstrate the appropriateness of the grammars for modeling RNA secondary structures by discussing its formal language and/or graph theoretic properties, including closure properties of TAG²_RNA and graph planarity of secondary structures generated by TAG²_RNA, the latter of which would provide a biologically reasonable constraint.