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Hairpin Structures in DNA Words

  • Lila Kari
  • Stavros Konstantinidis
  • Elena Losseva
  • Petr Sosík
  • Gabriel Thierrin
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3892)

Abstract

We formalize the notion of a DNA hairpin secondary structure, examining its mathematical properties. Two related secondary structures are also investigated, taking into the account imperfect bonds (bulges, mismatches) and multiple hairpins. We characterize maximal sets of hairpin-forming DNA sequences, as well as hairpin-free ones. We study their algebraic properties and their computational complexity. Related polynomial-time algorithms deciding hairpin-freedom of regular sets are presented. Finally, effective methods for design of long hairpin-free DNA words are given.

Keywords

Hairpin Structure Regular Language Free Word Pushdown Automaton Free Language 
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 2006

Authors and Affiliations

  • Lila Kari
    • 1
  • Stavros Konstantinidis
    • 2
  • Elena Losseva
    • 1
  • Petr Sosík
    • 3
    • 4
  • Gabriel Thierrin
    • 5
  1. 1.Department of Computer ScienceThe University of Western OntarioLondonCanada
  2. 2.Dept. of Mathematics and Computing ScienceSaint Mary’s UniversityHalifaxCanada
  3. 3.Facultad de InformáticaUniversidad Politécnica de MadridBoadilla del Monte, MadridSpain
  4. 4.Institute of Computer ScienceSilesian UniversityOpavaCzech Republic
  5. 5.Department of MathematicsThe University of Western OntarioLondonCanada

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