The complexity of string partitioning

Anne Condon; Ján Maňuch; Chris Thachuk

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arXiv · 1204.2201

The complexity of string partitioning

Anne Condon·Ján Maňuch·Chris Thachuk

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Abstract

Given a string $w$ over a finite alphabet $\Sigma$ and an integer $K$, can $w$ be partitioned into strings of length at most $K$, such that there are no \emph{collisions}? We refer to this question as the \emph{string partition} problem and show it is \NP-complete for various definitions of collision and for a number of interesting restrictions including $|\Sigma|=2$. This establishes the hardness of an important problem in contemporary synthetic biology, namely, oligo design for gene synthesis.

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Anne Condon, Ján Maňuch, Chris Thachuk. 2012-04-10. The complexity of string partitioning. https://arxiv.org/abs/1204.2201

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