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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Condon, A., Maňuch, J., Thachuk, C. (2008). Complexity of a Collision-Aware String Partition Problem and Its Relation to Oligo Design for Gene Synthesis. In: Hu, X., Wang, J. (eds) Computing and Combinatorics. COCOON 2008. Lecture Notes in Computer Science, vol 5092. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-69733-6_27
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DOI: https://doi.org/10.1007/978-3-540-69733-6_27
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