Molecules, Languages and Automata

Abstract

Molecular biology is full of linguistic metaphors, from the language of DNA to the genome as “book of life.” Certainly the organization of genes and other functional modules along the DNA sequence invites a syntactic view, which can be seen in certain tools used in bioinformatics such as hidden Markov models. It has also been shown that folding of RNA structures is neatly expressed by grammars that require expressive power beyond context-free, an approach that has even been extended to the much more complex structures of proteins. Processive enzymes and other “molecular machines” can also be cast in terms of automata. This paper briefly reviews linguistic approaches to molecular biology, and provides perspectives on potential future applications of grammars and automata in this field.