Theoretical and computational properties of transpositions

  • Authors:

  • Mark Daley;Ian Mcquillan;James M. Mcquillan;Kalpana Mahalingam

  • Affiliations:

  • Departments of Computer Science and Biology, University of Western Ontario, London, Canada N6A 5B7 and Department of Computer Science, University of Saskatchewan, Saskatoon, Canada S7N 5A9;Department of Computer Science, University of Saskatchewan, Saskatoon, Canada S7N 5A9;Department of Computer Science, Western Illinois University, Macomb, USA 61455-1390;Department of Computer Science, Indian Institute of Technology Madras, Chennai, India 600 036

  • Venue:
  • Natural Computing: an international journal
  • Year:
  • 2011

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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.