Complexity of a Collision-Aware String Partition Problem and Its Relation to Oligo Design for Gene Synthesis

  • Anne Condon
  • Ján Maňuch
  • Chris Thachuk
Part of the Lecture Notes in Computer Science book series (LNCS, volume 5092)


Artificial synthesis of long genes and entire genomes is achieved by self-assembly of DNA oligo fragments - fragments which are short enough to be generated using a DNA synthesizer. Given a description of the duplex to be synthesized, a computational challenge is to select the short oligos so that, once synthesized, they will self-assemble without error. In this paper, we show that a natural abstraction of this problem, the collision-aware string partition problem, is NP-complete.


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Copyright information

© Springer-Verlag Berlin Heidelberg 2008

Authors and Affiliations

  • Anne Condon
    • 1
  • Ján Maňuch
    • 2
  • Chris Thachuk
    • 1
  1. 1.University of British ColumbiaVancouverCanada
  2. 2.Simon Fraser UniversityBurnabyCanada

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