Lecture Notes in Computer Science, 2008, Volume 5092/2008, 265-275, DOI: 10.1007/978-3-540-69733-6_27

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

Anne Condon, Ján Maňuch and Chris Thachuk

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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.

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