The complexity of string partitioning

Authors:
Anne Condon;Ján Maňuch;Chris Thachuk
Affiliations:
Dept. of Computer Science, University of British Columbia, Vancouver, BC, Canada;Dept. of Computer Science, University of British Columbia, Vancouver, BC, Canada,Dept. of Mathematics, Simon Fraser University, Burnaby, BC, Canada;Dept. of Computer Science, University of British Columbia, Vancouver, BC, Canada
Venue:
CPM'12 Proceedings of the 23rd Annual conference on Combinatorial Pattern Matching
Year:
2012

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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.