Abstract
Given a string w over a finite alphabet Σ and an integer K, can w be partitioned into strings of length at most K, such that there are no collisions? We refer to this question as the string partition problem and show it is NP-complete for various definitions of collision and for a number of interesting restrictions including |Σ| = 2. This establishes the hardness of an important problem in contemporary synthetic biology, namely, oligo design for gene synthesis.
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Condon, A., Maňuch, J., Thachuk, C. (2012). The Complexity of String Partitioning. In: Kärkkäinen, J., Stoye, J. (eds) Combinatorial Pattern Matching. CPM 2012. Lecture Notes in Computer Science, vol 7354. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-31265-6_13
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DOI: https://doi.org/10.1007/978-3-642-31265-6_13
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