期刊
THEORETICAL COMPUTER SCIENCE
卷 410, 期 51, 页码 5374-5381出版社
ELSEVIER
DOI: 10.1016/j.tcs.2009.09.014
关键词
Shortest common superstring; Smoothed analysis; Polynomial time approximation scheme
资金
- NSERC RGPIN [238748]
- Canada Research Chair
- China NSF [60553001]
- China 973 [2007CB807900, 2007CB807901]
- China 863 [2008AA02Z313]
The shortest common superstring problem (SCS) has been extensively studied for its applications in string compression and DNA sequence assembly. Although the problem is known to be Max-SNP hard, the simple greedy algorithm performs extremely well in practice. To explain the good performance, previous researchers proved that the greedy algorithm is asymptotically optimal on random instances. Unfortunately, the practical instances in DNA sequence assembly are very different from the random instances. In this paper we explain the good performance of the greedy algorithm by using the smoothed analysis. We show that, for any given instance 1 of SCS, the average approximation ratio of the greedy algorithm on a small random perturbation oft is 1 + o(1). The perturbation defined in the paper is small and naturally represents the mutations of the DNA sequence during evolution. Due to the existence of the uncertain nucleotides in the output of a DNA sequencing machine, we also proposed the shortest common superstring with wildcards problem (SCSW). We prove that in the worst case SCSW cannot be approximated within the ratio n(1/7-epsilon), while the greedy algorithm still has 1 + o(1) smoothed approximation ratio. (C) 2009 Elsevier B.V. All rights reserved.
作者
我是这篇论文的作者
点击您的名字以认领此论文并将其添加到您的个人资料中。
推荐
暂无数据