The Complexity of String Partitioning

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


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.


Gene Synthesis Empty String Finite Alphabet Negative Strand Binary Alphabet 
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

  • 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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