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Theoretical and computational properties of transpositions

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Abstract

Transposable genetic elements are prevalent across many living organisms from bacteria to large mammals. Given the linear primary structure of genetic material, this process is natural to study from a theoretical perspective using formal language theory. We abstract the process of genetic transposition to operations on languages and study it combinatorially and computationally. It is shown that the power of such systems is large relative to the classic Chomsky Hierarchy. However, we are still able to algorithmically determine whether or not a string is a possible product of the iterated application of the operations.

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Acknowledgements

This research was supported by grants from the Natural Sciences and Engineering Research Council of Canada, institutional grants of the University of Saskatchewan and the University of Western Ontario and the SHARCNET Research Chairs Program.

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Authors and Affiliations

  1. Departments of Computer Science and Biology, University of Western Ontario, London, ON, N6A 5B7, Canada

    Mark Daley

  2. Department of Computer Science, University of Saskatchewan, Saskatoon, SK, S7N 5A9, Canada

    Mark Daley & Ian McQuillan

  3. Department of Computer Science, Western Illinois University, Macomb, IL, 61455-1390, USA

    James M. McQuillan

  4. Department of Computer Science, Indian Institute of Technology Madras, Chennai, 600 036, India

    Kalpana Mahalingam

Authors
  1. Mark Daley
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  2. Ian McQuillan
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  3. James M. McQuillan
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  4. Kalpana Mahalingam
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Correspondence to Mark Daley.

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Daley, M., McQuillan, I., McQuillan, J.M. et al. Theoretical and computational properties of transpositions. Nat Comput 10, 795–804 (2011). https://doi.org/10.1007/s11047-010-9207-z

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