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.
Categories: cs.CC cs.FL