DNA evolutionary linguistics and RNA structure modeling: A computational approach

In this paper, we are concerned with analyzing formal linguistic properties of DNA sequences in which a number of the language theoretic analysis on DNA sequences are established by means of computational methods. First, employing formal language theoretic framework, we consider a kind of an evolutionary problem of DNA sequences, asking (1) how DNA sequences were initially created and then evolved (grew up,) to be a language of certain complexity, and (2) what primitive constructs were minimally required for the process of evolution. In terms of formal linguistic concepts, we present several results that provide our view on these questions at a conceptual level. Based on the formal analysis on these biological questions, we then choose a certain type of tree generating grammars called Tree Adjunct Grammars (TAG) to attack the problem of modeling the secondary structure of RNA sequences. By proposing an extended model of TAGs, we demonstrate the usefulness of the grammars for modeling some typical RNA secondary structures including `pseudoknots', which suggests that TAG families as RNA grammars have a great potential for RNA secondary structure prediction.