Abstract
We define three operations on strings and languages suggested by the process of gene assembly in hypotrichous ciliates. This process is considered to be a prine example of DNA computing in vivo. This paper is devoted to some computational aspects of these operations from a formal language point of view. The closure of the classes of regular and context-free languages under these operations is settled. Then, we consider theld-macronuclear language of a given languageL, which consists of allld-macronuclear strings obtained from the strings ofL by iteratively applying the loop-direct repeat-excision. Finally, we discuss some open problems and further directions of research.
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Rudolf Freund: He received his master and doctor degree in computer science from the Vienna University of Technology, Austria, in 1980 and 1982, respectively. In 1986, he received his master degree in mathematics and physics from the University Vienna, Austria. In 1988 he joined the Vienna University of Technology in Austria, where he became an Associate Professor in September 1995. He has given various lectures in theoretical computer science, especially on formal languages and automata. His research interests include array and graph grammars, regulated rewritung, infinite words, syntactic pattern recognition, neural networks, and especially models and systems for biological computing. In these fields he is author of more than sixty scientific papers.
Carlos Martín-Vide: He is Professor and Head of the Research Group on Mathematical Linguistics at Rovira i Virgili University, Tarragona, Spain. His specialities are formal language theory and mathematical linguistics. His last volume edited is Where Mathematics, Computer Science, Linguistics and Biology Meet (Kluwer, 2001, with V. Mitrana). He published 150 papers in conference proceedings and journals such as: Acta Informatica, BioSystems. Computational Linguistics, Computers and Artificial Intelligence, Information Processing Letters, Information Sciences, International Journal of Computer Mathematics, New Generation Computing, Publicationes Mathematicae Debrecen, and Theoretical Computer Science. He is the editor-in-chief of the journal Grammars (Kluwer), and the chairman of the 1st International PhD School in Formal Languages and Applications (2001–2003).
Victor Mitrana, Ph.D.: He is Professor of Computer Science at the Faculty of Mathematics, University of Bucharest. He received his MSc and PhD from the University of Bucharest in 1986 and 1993, respectively. In 1999 he was awarded with the “Gheorghe Lazar” Prize for Mathematics of the Romanian Academy. His research interests include: formal language theory and applications, combinatorics on words, computational models inspired from biology, mathematical linguistics. In these areas, he published three books, more than 100 papers, and edited two books. He is an associate editor of “The Korean Journal of Computational and Applied Mathematics” and an editor of “Journal of Universal Computer Science”.
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Freund, R., Martín-Vide, C. & Mitrana, V. On some operations on strings suggested by gene assembly in ciliates. New Gener Comput 20, 279–293 (2002). https://doi.org/10.1007/BF03037361
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DOI: https://doi.org/10.1007/BF03037361