Universal DNA tag systems: a combinatorial design scheme
RECOMB '00 Proceedings of the fourth annual international conference on Computational molecular biology
Strand design for biomolecular computation
Theoretical Computer Science - Natural computing
Solution of a Satisfiability Problem on a Gel-Based DNA Computer
DNA '00 Revised Papers from the 6th International Workshop on DNA-Based Computers: DNA Computing
Stochastic Local Search Algorithms for DNA Word Design
DNA8 Revised Papers from the 8th International Workshop on DNA Based Computers: DNA Computing
Algorithmic self-assembly of dna
Algorithmic self-assembly of dna
Complexities for Generalized Models of Self-Assembly
SIAM Journal on Computing
Linear constructions for DNA codes
Theoretical Computer Science
Randomized fast design of short DNA words
ACM Transactions on Algorithms (TALG)
On codeword design in metric DNA spaces
Natural Computing: an international journal
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
Deterministic polynomial-time algorithms for designing short DNA words
TAMC'10 Proceedings of the 7th annual conference on Theory and Applications of Models of Computation
Flexible word design and graph labeling
ISAAC'06 Proceedings of the 17th international conference on Algorithms and Computation
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Designing short DNA words is a problem of constructing a set (i.e., code) of n DNA strings (i.e., words) with the minimum length such that the Hamming distance between each pair of words is at least k and the n words satisfy a set of additional constraints. This problem has applications in, e.g., DNA self-assembly and DNA arrays. Previous works include those that extended results from coding theory to obtain bounds on code and word sizes for biologically motivated constraints and those that applied heuristic local searches, genetic algorithms, and randomized algorithms. In particular, Kao, Sanghi, and Schweller [16] developed polynomial-time randomized algorithms to construct n DNA words of length within a multiplicative constant of the smallest possible word length (e.g., 9@?max{logn,k}) that satisfy various sets of constraints with high probability. In this paper, we give deterministic polynomial-time algorithms to construct DNA words based on derandomization techniques. Our algorithms can construct n DNA words of shorter length (e.g., 2.1logn+6.28k) and can satisfy the same sets of constraints as the words constructed by the algorithms of Kao et al.. Furthermore, we extend these new algorithms to construct words that satisfy a larger set of constraints for which the algorithms of Kao et al. do not work.