DNA Sequence Design by Dynamic Neighborhood Searches
DNA Sequence Design by Dynamic Neighborhood Searches
复制标题
DOI：
10.1007/11925903_12
复制
发表时间：
2006-05
期刊：
影响因子：
--
通讯作者：
Suguru Kawashimo;H. Ono;K. Sadakane;M. Yamashita
中科院分区：
文献类型：
--
作者：
Suguru Kawashimo;H. Ono;K. Sadakane;M. Yamashita
我们提出了一个基于局部搜索的算法来设计DNA序列集，满足几个组合约束的汉明距离标准。为了处理局部搜索中的约束，我们采用了精心设计的（和动态的）邻域搜索框架，称为可变邻域搜索（VNS）和可变深度搜索（VDS）。虽然我们的算法可以处理许多类型的汉明距离为基础的约束，并易于扩展（例如，也适用于其他约束），在计算实验中，我们成功地产生更好的序列集比现有的方法产生的更指定的约束。
We propose a local-search based algorithm to design DNA sequence sets that satisfy several combinatorial constraints about hamming-distance criteria. To deal with the constraints in the local search, we adopt elaborate (and dynamic) neighborhood search frameworks called the Variable Neighborhood Search (VNS) and the Variable Depth Search (VDS). Although our algorithm can deal with many types of hamming distance-based constraints and is easy to extend (eg, also applicable for other constraints), in computational experiments, we succeeded in generating better sequence sets than the ones generated by exiting methods of more specified constraints.