Ming-Yang Kao
Abstract
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 self-assembly and DNA computing. 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 article 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 simple randomized 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 with high probability. 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.
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Index Terms
- Randomized fast design of short DNA words
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Reviews
Pietro Hiram Guzzi
The design of short DNA words-that is, the design of sets of DNA strings that satisfy a number of constraints-is a key problem in many areas. Kao, Sanghi, and Schweller present in this paper a novel formulation of this problem as an optimization problem and propose randomized algorithms to solve it. The proposed solution has a sound formulation in terms of optimization and is computationally tractable, being polynomial in most cases. The main contribution of the paper is the original formulation of the problem that could motivate further discussions. Considering that the paper is designed to be read by an expert audience, it has a clear structure and a clear formulation. Online Computing Reviews Service
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