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Iterated Hairpin Completions of Non-crossing Words

  • Lila Kari
  • Steffen Kopecki
  • Shinnosuke Seki
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7147)

Abstract

Iterated hairpin completion is an operation on formal languages that is inspired by the hairpin formation in DNA biochemistry. Iterated hairpin completion of a word (or more precisely a singleton language) is always a context-sensitive language and for some words it is known to be non-context-free. However, it is unknown whether regularity of iterated hairpin completion of a given word is decidable. Also the question whether iterated hairpin completion of a word can be context-free but not regular was asked in literature. In this paper we investigate iterated hairpin completions of non-crossing words and, within this setting, we are able to answer both questions. For non-crossing words we prove that the regularity of iterated hairpin completions is decidable and that if iterated hairpin completion of a non-crossing word is not regular, then it is not context-free either.

Keywords

Single Strand Regular Language Minimal Index Hairpin Formation Hamiltonian Path Problem 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Lila Kari
    • 1
  • Steffen Kopecki
    • 1
    • 2
  • Shinnosuke Seki
    • 3
  1. 1.Department of Computer ScienceUniversity of Western OntarioLondonCanada
  2. 2.Institute for Formal Methods in Computer ScienceUniversity of StuttgartGermany
  3. 3.Department of Systems Biosciences for Drug Discovery Graduate School of Pharmaceutical SciencesKyoto UniversityJapan

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