Hairpin Completion Versus Hairpin Reduction

  • Florin Manea
  • Victor Mitrana
Part of the Lecture Notes in Computer Science book series (LNCS, volume 4497)

Abstract

We define the hairpin reduction as the inverse operation of a formal operation on words and languages suggested by DNA biochemistry, namely the hairpin completion, introduced in [3]. We settle the closure properties of some classes in the Chomsky hierarchy as well as some complexity classes under the non-iterated version of the hairpin reduction, in comparison with the hairpin completion. Then an algorithm that decides whether or not a regular language coincides with its primitive hairpin root is presented. Finally, we discuss a cubic time algorithm for computing the common ancestors of two given words. This algorithm may be used also for computing the closest or farthest primitive hairpin root of a given word.

Keywords

DNA computing formal languages hairpin completion hairpin reduction primitive hairpin root 

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Copyright information

© Springer-Verlag Berlin Heidelberg 2007

Authors and Affiliations

  • Florin Manea
    • 1
  • Victor Mitrana
    • 1
    • 2
  1. 1.Faculty of Mathematics and Computer Science, University of Bucharest, Str. Academiei 14, 70109, BucharestRomania
  2. 2.Research Group in Mathematical Linguistics, Rovira i Virgili University, Pl. Imperial Tarraco 1, 43005, TarragonaSpain

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