The stimulus for the development of the theory presented in this chapter is the string behaviors exhibited by the group of molecules often referred to collectively as the informational macromolecules. These include the molecules that play central roles in molecular biology and genetics: DNA, RNA, and the polypeptides. The discussion of the motivation for the generative systems is focused here on the recombinant behaviors of double stranded DNA molecules made possible by the presence of specific sets of enzymes. The function of this introduction is to provide richness to the reading of this chapter. It indicates the potential for productive interaction between the systems discussed and molecular biology, biotechnology, and DNA computing. However, the theory developed in this chapter can stand alone. It does not require a concern for its origins in molecular phenomena. Accordingly, only the most central points concerning the molecular connection are given here. An appendix to this chapter is included for those who wish to consider the molecular connection and possible applications in the biosciences. Here we present only enough details to motivate each term in the definition of the concept of a splicing rule that is given in the next section. The splicing rule concept is the foundation for the present chapter.

Language theory and molecular genetics: generative mechanisms suggested by DNA recombination

attributes, 5 acceptation style, 25 accepting grammar mode, 19 Acoi, 8 Acoi image algebra, 120 Admire, 5 ALGOL 60, 45 alternative production rules, 20, 46 ambiguity, 5, 20, 68 ambiguous feature grammar systems, 39 analysis, 57 AND/OR-graph, 20 annotation extraction algorithm, 5 annotation subsystem, 3 annotations, 4 anonymous symbol, 48 artificial language, 18 atom, 32, 48 atom symbols, 32 atom type, 48 attribute grammars, 97 Australian Open, 128 automaton, 66 auxiliary tree, 82 axiom, 15 back propagation neural network, 57 basic feature grammar system, 29 batch learning algorithms, 58 bidirectional grammars, 19 binary association table (BAT), 99 blackboard architecture, 24 blackbox detector, 56 bottom-up parsing algorithm, 69 bounds, 54 breadth-first parsing algorithm, 70 Chomsky hierarchy, 16 classifier, 57, 95 COBRA, 5, 128 compositional semantics, 5 concept, 6, 54 conceptual level, 126 conditional feature grammar system, 38 conditional grammars, 22 constant, 54 context, 88 context dependency, 6, 113 context globalization, 91 context localization, 91 context-free (CF) grammars, 17 context-sensitive (CS) grammars, 16 controlled named disjunction, 40 controller named disjunction, 40 cooperating distributed (CD) grammar sys- tems, 24 crossed agreements, 17 data repository, 135 database management system (DBMS), 4 dataflow languages, 43 deadlock, 36, 61, 91, 96 deadlock prevention, 36 decision rule, 6, 54, 55 decomposed storage model (DSM), 99 delta operation, 19 dependencies, 33 dependency graph, 111 depth-first parsing algorithm, 69 derivation, 18 derivation mode, 25 derived features, 5 detector, 28, 49 detector confidence, 41, 52

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Feature grammar systems. Incremental maintenance of indexes to digital media warehouses

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

Language-theoretic aspects of DNA complementarity

Lindenmayer and DNA: Watson-Crick D0L Systems.

Lindenmayer and DNA: Watson-Crick D0L systems

Accepting Cooperating Distributed Grammar Systems with Terminal Derivation.

We consider the following new way of generating a language: start with a string w and a given set of insertion contexts (u,v); if uv appears as a substring of w, then we can insert in between u and v any substring of w which starts with v and ends with u (hence preserving the link restriction encoded by (u,v)); iterating this operation, we get a language. Many variants can be imagined, concerning the place where the insertion is performed (free, leftmost, etc.), and the string to be inserted (any one, a prefix of the current string, a minimal or a maximal prefix, a minimal or a maximal substring, the whole string, etc.). We investigate here ten such variants, for the case when we have only one insertion context, namely of the form (a,b), where a and b are symbols. The corresponding families of languages are compared to each other (all the relationships are settled), as well as to families in Chomsky hierarchy. A series of topics for further research are pointed out.

Valeria Mihalache

Papers

Language-theoretic aspects of DNA complementarity

Lindenmayer and DNA: Watson-Crick D0L Systems.

Lindenmayer and DNA: Watson-Crick D0L systems

Accepting Cooperating Distributed Grammar Systems with Terminal Derivation.

Generating Strings by Replication: A Simple Case