Modeling RNA Secondary Structures Using Tree Grammars

This paper proposes a grammatical tool, called tree adjunct grammar with tag for RNA ( denoted by TAG 2 RNA ), for representing secondary structures of RNAs, and shows some example TAG 2 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 TAG 2 RNA and graph planarity of secondary structures generated by TAG 2 RNA , the latter of which would provide a biologically reasonable constraint.