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Splicing Representations of Strictly Locally Testable Languages
 Discrete Applied Math
, 1998
"... The relationship between the family SH of simple splicing languages, which was recently introduced by A. Mateescu and coauthors, and the family SLT of strictly locally testable languages is clarified by establishing an ascending hierarchy of families fS i H : i \Gamma1g of splicing languages for ..."
Abstract

Cited by 9 (2 self)
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The relationship between the family SH of simple splicing languages, which was recently introduced by A. Mateescu and coauthors, and the family SLT of strictly locally testable languages is clarified by establishing an ascending hierarchy of families fS i H : i \Gamma1g of splicing languages for which SH = S1H and the union of the families is the family SLT . A procedure is given which, for an arbitrary regular language L, determines whether L is in SLT and, when L is in SLT , specifies constructively the smallest family in the hierarchy to which L belongs. Examples are given of sets of restriction enzymes for which the action on DNA molecules is naturally represented by splicing systems of the types discussed. Key words. Splicing systems, H Systems, DNA Computing, local testability, regular languages, restriction enzymes 1 Introduction The splicing system concept was introduced in [6] as a formal device for the generation of languages and as a formal model of specific forms ...
Splicing to the limit
 Lecture Notes in Computer Science
"... Summary. We consider the result of a wet splicing procedure after the reaction has run to its completion, or limit, and we try to describe the molecules that will be present at this final stage. In language theoretic terms the splicing procedure is modeled as an H system, and the molecules that we w ..."
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Summary. We consider the result of a wet splicing procedure after the reaction has run to its completion, or limit, and we try to describe the molecules that will be present at this final stage. In language theoretic terms the splicing procedure is modeled as an H system, and the molecules that we want to consider correspond to a subset of the splicing language which we call the limit language. We give a number of examples, including one based on differential equations, and we propose a definition for the limit language. With this definition we prove that a language is regular if and only if it is the limit language of a reflexive and symmetric splicing system. 1
Locally Aligned Terminal Distinguishable Languages And Identification of Proteins
, 2002
"... Grammatical Inference is the problem of learning a formal grammar that characterizes a set of strings over an alphabet. In particular, the problem of inferring regular grammars from positive data is considered in this paper. In the framework of identification in the limit, subfamilies of the family ..."
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Grammatical Inference is the problem of learning a formal grammar that characterizes a set of strings over an alphabet. In particular, the problem of inferring regular grammars from positive data is considered in this paper. In the framework of identification in the limit, subfamilies of the family of regular languages have been defined in the literature. These include Strictly Locally Testable Languages(SLT) and Terminal Distinguishable Regular Languages (TDRL). TDRL's have been shown to possess many desirable properties for inference. SLT languages have been applied to protein sequence analysis. When dealing with biological sequences, local alignment issues become important. In this paper, a framework has been proposed for introducing local alignment considerations into grammar inference models and a learning algorithm has been given for a family defined as Locally Aligned TDRL. Results of application of the algorithm to protein sequence data and comparison with SLT are presented. Experimentally, it is inferred that the generalization of LATDRL is not affected by noise that is present in the data and the amount of generalization can be controlled by an input parameter.
Enzyme Optimization For Next Level Molecular Computing
"... The main concept of molecular computing depends on DNA selfassembly abilities and on modifying DNA with the help of enzymes during genetic operations. In the typical DNA computing a sequence of operations executed on DNA strings in parallel is called an algorithm, which is also determined by a mode ..."
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The main concept of molecular computing depends on DNA selfassembly abilities and on modifying DNA with the help of enzymes during genetic operations. In the typical DNA computing a sequence of operations executed on DNA strings in parallel is called an algorithm, which is also determined by a model of DNA strings. This methodology is similar to the soft hardware specialized architecture driven here by heating, cooling and enzymes, especially polymerases used for copying strings. As it is described in this paper the polymerase Taq properties are changed by modifying its DNA sequence in such a way that polymerase side activities together with peptide chains, responsible for destroying amplified strings, are cut off. Thus, it introduces the next level of molecular computing. The genetic operation execution succession and the given molecule model with designed nucleotide sequences produce computation results and additionally they modify enzymes, which directly influence on the computation process. The information flow begins to circulate. Additionally, such optimized enzymes are more suitable for nanoconstruction, because they have only desired characteristics. The experiment was proposed to confirm the possibilities of the suggested implementation.
Deciding whether a Regular Language is Generated by a Splicing System ⋆
"... Abstract. Splicing as a binary word/language operation is inspired by the DNA recombination under the action of restriction enzymes and ligases, and was first introduced by Tom Head in 1987. Shortly thereafter, it was proven that the languages generated by (finite) splicing systems form a proper sub ..."
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Abstract. Splicing as a binary word/language operation is inspired by the DNA recombination under the action of restriction enzymes and ligases, and was first introduced by Tom Head in 1987. Shortly thereafter, it was proven that the languages generated by (finite) splicing systems form a proper subclass of the class of regular languages. However, the question of whether or not one can decide if a given regular language is generated by a splicing system remained open. In this paper we give a positive answer to this question. Namely, we prove that, if a language is generated by a splicing system, then it is also generated by a splicing system whose size is a function of the size of the syntactic monoid of the input language, and which can be effectively constructed. 1
Deciding if a Regular Language is Generated by a Splicing System ∗
, 2011
"... Splicing as a binary word/language operation is inspired by the DNA recombination under the action of restriction enzymes and ligases, and was first introduced by Tom Head in 1987. Shortly after, it was proven that the languages generated by (finite) splicing systems form a proper subclass of the cl ..."
Abstract
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Splicing as a binary word/language operation is inspired by the DNA recombination under the action of restriction enzymes and ligases, and was first introduced by Tom Head in 1987. Shortly after, it was proven that the languages generated by (finite) splicing systems form a proper subclass of the class of regular languages. However, the question of whether or not one can decide if a given regular language is generated by a splicing system remained open. In this paper we give a positive answer to this question. We namely prove that if a language is generated by a splicing system, then it is also generated by a splicing system whose size is a function of the size of the syntactic monoid of the input language, and which can be effectively constructed. 1