短DNA字设计的确定性多项式时间算法
Deterministic Polynomial-Time Algorithms for Designing Short DNA Words
摘要：
设计短DNA字是构建集合的问题（即，代码）的n个DNA串（即，字），使得每对字之间的汉明距离至少为k，并且n个字满足一组附加约束。这个问题有应用，例如，DNA自组装和DNA阵列。以前的工作包括那些扩展结果从编码理论获得的界限代码和字的大小为生物学动机的限制和那些应用启发式局部搜索，遗传算法，和随机算法。特别地，Kao、Sanghi和Schweller（2009）开发了多项式时间随机算法来构建长度在最小可能字长的乘法常数内的n个DNA字（例如，9 max{log n，k}），其以高概率满足各种约束集合。在本文中，我们给出了确定性的多项式时间算法来构建DNA字的基础上去随机化技术。我们的算法可以构建n个较短长度的DNA字（例如，2.1 log n + 6.28 k），并满足相同的约束条件，由算法的高等人的话。此外，我们扩展这些新的算法，以构建满足一个更大的约束条件的算法的高等人的话。不工作。
英文摘要：
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 (2009) 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{log n, 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., 2.1 log n + 6.28 k) and 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.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
