短DNA字的随机快速设计
Randomized Fast Design of Short DNA Words
摘要：
我们认为，有效地设计集（代码）的等长DNA字符串（字），满足一定的组合约束的问题。这个问题有许多动机，包括DNA计算和DNA自组装。以前的工作已经扩展了编码理论的结果，以获得新的生物动机的限制代码大小的界限，并已应用启发式局部搜索和遗传算法技术的代码设计。本文提出了一种自然的优化配方的DNA代码设计问题，其目标是设计n个字符串，满足一组给定的约束条件，同时最小化的字符串的长度。对于多组约束条件，我们提供了高概率算法，该算法在n和任何给定的约束参数中以时间多项式运行，并输出长度在最佳常数因子内的字符串。据我们所知，这项工作是第一次考虑这种类型的优化问题的背景下，DNA代码设计。
英文摘要：
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.
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