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Duplication in DNA Sequences

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Book cover Algorithmic Bioprocesses

Part of the book series: Natural Computing Series ((NCS))

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Abstract

The duplication and repeat-deletion operations are the basis of a formal language theoretic model of errors that can occur during DNA replication. During DNA replication, subsequences of a strand of DNA may be copied several times (resulting in duplications) or skipped (resulting in repeat-deletions). As formal language operations, iterated duplication and repeat-deletion of words and languages have been well studied in the literature. However, little is known about single-step duplications and repeat-deletions. In this paper, we investigate several properties of these operations, including closure properties of language families in the Chomsky hierarchy and equations involving these operations. We also make progress toward a characterization of regular languages that are generated by duplicating a regular language.

This research was supported by Grant-in-Aid for Scientific Research No. 19-07810 by the Japan Society for the Promotion of Sciences and Research Grant No. 015 by Kyoto Sangyo University to M.I., and The Natural Sciences and Engineering Council of Canada Discovery Grant and Canada Research Chair Award to L.K.

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Author information

Authors and Affiliations

  1. Department of Mathematics, Faculty of Science, Kyoto Sangyo University, Kyoto, 603-8555, Japan

    Masami Ito

  2. Department of Computer Science, University of Western Ontario, London, Ontario, N6A 5B7, Canada

    Lila Kari, Zachary Kincaid & Shinnosuke Seki

  3. Department of Mathematics, University of Western Ontario, London, Ontario, N6A 5B7, Canada

    Zachary Kincaid

Authors
  1. Masami Ito
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  2. Lila Kari
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  3. Zachary Kincaid
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  4. Shinnosuke Seki
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Corresponding author

Correspondence to Shinnosuke Seki .

Editor information

Editors and Affiliations

  1. Dept. Computer Science, University of British Columbia, Main Mall 201-2366, Vancouver, V6T 1Z4, Canada

    Anne Condon

  2. Dept. Applied Mathematics, Weizmann Institute of Science, Rehovot, 76100, Israel

    David Harel

  3. Leiden Inst. Advanced Computer Science, Leiden University, Niels Bohrweg 1, Leiden, 2333 CA, Netherlands

    Joost N. Kok

  4. Turku Centre for Computer Science, Lemminkaisenkatu 14 A, Turku, 20520, Finland

    Arto Salomaa

  5. Computer Science, Computation,, California Inst. of Technology, Pasadena, 91125, U.S.A.

    Erik Winfree

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Ito, M., Kari, L., Kincaid, Z., Seki, S. (2009). Duplication in DNA Sequences. In: Condon, A., Harel, D., Kok, J., Salomaa, A., Winfree, E. (eds) Algorithmic Bioprocesses. Natural Computing Series. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-88869-7_4

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  • DOI: https://doi.org/10.1007/978-3-540-88869-7_4

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  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-88868-0

  • Online ISBN: 978-3-540-88869-7

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