In this paper we introduce a variation of Watson-Crick automata in which both heads read the doubled DNA strand form 5' to 3'. The sensing version of these automata recognize exactly the linear context-free languages. The deterministic version is not so powerful, but all fixed-rated linear (for instance even-linear) languages can be accepted by them. Relation to other variations of Watson-Crick automata and pushdown automata are presented. The full-reading version of sensing 5′ → 3′ automata recognizes non context-free languages as well.

On 5' → 3' sensing Watson-Crick finite automata

This paper surveys some known results in Watson-Crick automata theory. In particular, we concentrate on the computational power, complexity measures, decidability problems, and systems of Watson-Crick automata working together on the same input. This selection of topics is not exhaustive, reflecting the research interests of the authors. A series of open problems and questions is also included.

A Short Survey on Watson-Crick Automata.

On the descriptional complexity of Watson-Crick automata

Structural analysis of regulatory DNA sequences using grammar inference and Support Vector Machine

In [4, page166], it is asked what influence the complementarity relation plays as far as the expressiveness of sticker systems and Watson-Crick automata are concerned. Here, we give the answer: (almost) none! More precisely, we show that every language L of a sticker system or a Watson-Crick automaton is the language of such a system with a one-to-one complementarity relation. Our second group of results shows that L is the inverse block coding of a language from the same family over any nontrivial fixed complementarity relation. Finally, we prove that any Watson-Crick automaton can be transformed into an equivalent simple and all-final one. This implies the collapse of parts of the hierarchy introduced in [4].

The role of the complementarity relation in Watson-Crick automata and sticker systems

Watson-Crick ω-automata are finite automata working with infinite double-stranded words, where the two strands relate to each other through a complementary relation inspired by the DNA complementarity. There are several natural possibilities to define such automata, in particular to define the acceptance condition for such infinit double-stranded words. We present here several results on the equivalence of Buchi, Rabin, Streett, and Muller-like acceptance conditions. We prove that these acceptance conditions are equivalent for nondeterministic Watson-Crick ω-automata. For deterministic automata, we prove that the four conditions are equivalent for nonempty stateless automata, while the general case remains open. We also investigate the relationship between the classes of languages accepted by several types of Watson-Crick ω-automata.

Elena Petre

Papers

Watson-Crick ω-automata