The complexity of string partitioning

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.

14 pages main text + 13 pages appendix. Full version with proofs of an article appearing in the Proceedings of the 23rd Annual Symposium on Combinatorial Pattern Matching (CPM 2012), Helsinki, Finland, July 2012