English

The complexity of string partitioning

Computational Complexity 2012-04-11 v1 Formal Languages and Automata Theory

Abstract

Given a string ww over a finite alphabet Σ\Sigma and an integer KK, can ww be partitioned into strings of length at most KK, 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 Σ=2|\Sigma|=2. This establishes the hardness of an important problem in contemporary synthetic biology, namely, oligo design for gene synthesis.

Keywords

Cite

@article{arxiv.1204.2201,
  title  = {The complexity of string partitioning},
  author = {Anne Condon and Ján Maňuch and Chris Thachuk},
  journal= {arXiv preprint arXiv:1204.2201},
  year   = {2012}
}

Comments

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

R2 v1 2026-06-21T20:47:29.038Z