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Preventing Undesirable Bonds Between DNA Codewords

  • Lila Kari
  • Stavros Konstantinidis
  • Petr Sosík
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3384)

Abstract

The input data for DNA computing must be encoded into the form of single or double DNA strands. As complementary parts of single strands can bind together forming a double-stranded DNA sequence, one has to impose restrictions on these sets of DNA words (=languages) to prevent them from interacting in undesirable ways. We recall a list of known properties of DNA languages which are free of certain types of undesirable bonds. Then we introduce a general framework in which we can characterize each of these properties by a solution of a uniform formal language inequation. This characterization allows us among others to construct (i) a uniform algorithm deciding in polynomial time whether a given DNA language possesses any of the studied properties, and (ii) in many cases also an algorithm deciding whether a given DNA language is maximal with respect to the desired property.

Keywords

Regular Language Quadratic Time Maximal Subset Phrase Degree Language Property 
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 2005

Authors and Affiliations

  • Lila Kari
    • 1
  • Stavros Konstantinidis
    • 2
  • Petr Sosík
    • 1
    • 3
  1. 1.Department of Computer ScienceThe University of Western OntarioLondonCanada
  2. 2.Dept. of Mathematics and Computing ScienceSaint Mary’s UniversityHalifax, Nova ScotiaCanada
  3. 3.Institute of Computer ScienceSilesian UniversityOpavaCzech Republic

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