Universal DNA tag systems: a combinatorial design scheme
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Introduction to Algorithms
Strand design for biomolecular computation
Theoretical Computer Science - Natural computing
Stochastic Local Search Algorithms for DNA Word Design
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
Complexities for generalized models of self-assembly
SODA '04 Proceedings of the fifteenth annual ACM-SIAM symposium on Discrete algorithms
Hybrid randomised neighbourhoods improve stochastic local search for DNA code design
AI'03 Proceedings of the 16th Canadian society for computational studies of intelligence conference on Advances in artificial intelligence
The Closest Pair Problem under the Hamming Metric
COCOON '09 Proceedings of the 15th Annual International Conference on Computing and Combinatorics
Flexible word design and graph labeling
ISAAC'06 Proceedings of the 17th international conference on Algorithms and Computation
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We consider the problem of efficiently designing sets (codes) of equal-length DNA strings (words) that satisfy certain combinatorial constraints. This problem has numerous motivations including DNA computing and DNA self-assembly. Previous work has extended results from coding theory to obtain bounds on code size for new biologically motivated constraints and has applied heuristic local search and genetic algorithm techniques for code design. This paper proposes a natural optimization formulation of the DNA code design problem in which the goal is to design n strings that satisfy a given set of constraints while minimizing the length of the strings. For multiple sets of constraints, we provide high-probability algorithms that run in time polynomial in n and any given constraint parameters, and output strings of length within a constant factor of the optimal. To the best of our knowledge, this work is the first to consider this type of optimization problem in the context of DNA code design.