Abstract
The process of gene unscrambling in ciliates (a type of unicellular protozoa), which accomplishes the dificult task of re-arranging gene segments in the correct order and deleting non-coding sequences from an “encrypted” version of a DNA strand, has been modeled and studied so far from the point of view of the computational power of the DNA bio-operations involved. Here we concentrate on a different aspect of the process, by considering only the linear version of the bio-operations, that do not involve thus any circular strands, and by studying the resulting formal operations from a purely language theoretic point of view. We namely investigate closure operations of language families under the mentioned bio-operations and study language equations involving them. Among the problems addressed, we study the decidability of existence of solutions to equations of the form L ◊ Y = R, X ◊ L = R where L and R are given languages, X and Y are unknowns, and ◊ signifies one of the defined bio-operations.
Research supported by Natural Sciences and Engineering Council of Canada Grants. All correspondence to L.K.
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References
J.M. Autebert, J. Berstel, L. Boasson 1997. Context-free languages and Pushdown Automata. Handbook of formal languages, 1: 111–174, Springer, Berlin.
J. Dassow, V. Mitrana, A. Salomaa. 2002. Operations and language generating devices suggested by the genome evolution. Theoretical Computer Science, 270:701–738.
A. Ehrenfeucht, D.M. Prescott, G. Rozenberg. 2001. Computational aspects of gene (un)scrambling is ciliates. In Evolution as Computation (L.F. Landweber, E. Winfree eds.) Springer-Verlag, Berlin, Heidelberg, 45–86.
S. Ginsburg. 1975. Algebraic and Automata-Theoretic Properties of Formal Languages. North-Holland, Amsterdam.
L. Kari, L.F. Landweber. 2000. Computational power of gene rearrangment In DNA5, DIMACS series in Discrete Mathematics and Theoretical Computer Science)(E. Winfree, D. Gifford eds.), American Mathematical Society, 54: 207–216.
L. Kari, G. Thierrin. 1996. Contextual insertions/deletions and computability. Information and Computation, 131: 47–61.
L. Kari. 1992. Insertion and deletion of words: determinism and reversibility. Lecture Notes in Computer Science, 629:315–327.
L. Kari. 1994. On language equations with invertible operations. Theoretical Computer Science, 132: 129–150.
L. Kari. 1991. On insertions and deletions in formal languages. PhD thesis, University of Turku, Finland.
L.F. Landweber, L. Kari. 1999. The evolution of cellular computing: nature’s solutions to a computational problem. DNA4 Biosystems (L. Kari, H. Rubin, D.H. Wood eds.), Elsevier, 52(1–3):3–13.
I. Petre, A. Ehrenfeucht, T. Harju and G. Rozenberg. 2002. Patterns of micronuclear genes in cilliates. In DNA7, Lecture Notes in Computer Science (N. Jonoska, N. Seeman eds.), Springer-Verlag, 2340: 279–289.
D.M. Prescott. 1992. Cutting, splicing, reordering, and elimination of DNA sequences in hypotrichous ciliates. BioEssays, 14(5): 317–324.
D.M. Prescott. 1992. The unusual organization and processing of genomic DNA in hypotrichous ciliates. Trends in Genet., 8:439–445.
D.M. Prescott. 2000. Genome gymnastics: Unique modes of DNA evolution and processing in ciliates. Nature Reviews Genetics, 1:191–198.
D.M. Prescott, A. Ehrenfeucht, G. Rozenberg. 2001. Molecular operations for DNA processing in hypotrichous ciliates. To appear in European Journal of Protistology.
A. Salomaa. 1973. Formal languages, Academic Press, New York.
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Daley, M., Kari, L. (2003). Some Properties of Ciliate Bio-operations. In: Ito, M., Toyama, M. (eds) Developments in Language Theory. DLT 2002. Lecture Notes in Computer Science, vol 2450. Springer, Berlin, Heidelberg. https://doi.org/10.1007/3-540-45005-X_10
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DOI: https://doi.org/10.1007/3-540-45005-X_10
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