The complexity of string partitioning
Computational Complexity
2012-04-11 v1 Formal Languages and Automata Theory
Abstract
Given a string over a finite alphabet and an integer , can be partitioned into strings of length at most , 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 . 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