The Complexity of String Partitioning

  • Anne Condon
  • Ján Maňuch
  • Chris Thachuk
Part of the Lecture Notes in Computer Science book series (LNCS, volume 7354)

Abstract

Given a string w over a finite alphabet Σ and an integer K, can w be partitioned into strings of length at most K, such that there are no collisions? We refer to this question as the string partition problem and show it is NP-complete for various definitions of collision and for a number of interesting restrictions including |Σ| = 2. This establishes the hardness of an important problem in contemporary synthetic biology, namely, oligo design for gene synthesis.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2012

Authors and Affiliations

  • Anne Condon
    • 1
  • Ján Maňuch
    • 1
    • 2
  • Chris Thachuk
    • 1
  1. 1.Dept. of Computer ScienceUniversity of British ColumbiaVancouverCanada
  2. 2.Dept. of MathematicsSimon Fraser UniversityBurnabyCanada

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