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

  • Authors:

  • Anne Condon;Ján Maňuch;Chris Thachuk

  • Affiliations:

  • University of British Columbia, Vancouver, Canada BC V6T 1Z4;Simon Fraser University, Burnaby, Canada BC V5A 1S7;University of British Columbia, Vancouver, Canada BC V6T 1Z4

  • Venue:
  • COCOON '08 Proceedings of the 14th annual international conference on Computing and Combinatorics
  • Year:
  • 2008

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Abstract

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.