On some operations on strings suggested by gene assembly in ciliates
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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.
KeywordsMolecular Computing gac-Scheme Macronuclear String
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- 1).Dassow, J. and Mitrana, V., “On Some Operations Suggested by Genome Evolution,”in Proc. of Second Pacific Symposium on Biocomputing (Altman, R. B., Dunker, A. K., Hunter, L. and Klein, T., eds.), World Scientific, pp. 97–108, 1997.Google Scholar
- 4).Ehrenfeucht, A., Prescott, D. M. and Rozenberg, G., “Computational Aspects of Gene (un)Scrambling in Cilitates,”in Evolution as Computation (Landweber, L. and Winfree, E., eds.), Springer Verlag, Berlin, pp. 45–86, 2001.Google Scholar
- 5).Ehrenfeucht, A., Petre, I, Prescott, D. M. and Rozenberg, G., “Universal and Simple Operations for Gene Assembly in Ciliates,”in Where Mathematics, Computer Science, Linguistics and Biology Meet (Martín-Vide, C. and Mitrana, V., eds.), Kluwer Academic, Dordrecht, pp. 329–343, 2000.Google Scholar
- 6).Ehrenfeucht, A., Harju, T., Petre, I. and Rozenberg, G., “Patterns of Micronuclear Genes in Ciliates,”in Proc. of the 7th DIMACS meeting on DNA based computers, Tampa, Florida, pp. 33–42, 2001.Google Scholar
- 9).Landweber, L. F. and Kari, L., “Universal Molecular Computation in Ciliates,” to appear inEvolution as Computation (Landweber, L. and Winfree, E., eds.), Springer Verlag, Berlin.Google Scholar
- 12).Searls, D. B., “The Computational Linguistics of Biological Sequences,”Artificial Intelligence and Molecular Biology (Hunter, L., ed.), AAAI Press, The MIT Press, pp. 47–120, 1993.Google Scholar
- 14).Yokomori, T. and Kobayashi, S., “DNA Evolutionary Linguistics and RNA Structure Modelling: a Computational Approach,”in IEEE Symp. on Intelligence in Neural and Biological Systems, IEEE Computer Society Press, pp. 38–45, 1995.Google Scholar