Complexity of a collision-aware string partition problem and its relation to oligo design for gene synthesis

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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. © 2008 Springer-Verlag Berlin Heidelberg.

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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 Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) (Vol. 5092 LNCS, pp. 265–275). https://doi.org/10.1007/978-3-540-69733-6_27

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