Constrained Pairwise and Center-Star Sequences Alignment Problems
文献类型：期刊论文
| 作者 | Yong Zhang; Joseph Wun-Tat Chan; Francis Y. L. Chin; Hing-Fung Ting; Deshi Ye; Feng Zhang; Jianyu Shi |
| 刊名 | Journal of Combinatorial Optimization
 |
| 出版日期 | 2016 |
| 英文摘要 | Sequence alignment is a fundamental problem in computational biology, which is also important in theoretical computer science. In this paper, we consider the problem of aligning a set of sequences subject to a given constrained sequence. Given two sequences A = a1a2 . . . an and B = b1b2 . . . bn with a given distance function and a constrained sequence C = c1c2 . . . ck , our goal is to find the optimal sequence alignment of A and B w.r.t. the constraint C.We investigate several variants of this problem. If C = ck , i.e., all characters in C are same, the optimal constrained pairwise sequence alignment can be solved in O(min{kn2, (t − k)n2}) time, where t is the minimum number of occurrences of character c in A and B. If in the final alignment, the alignment score between any two consecutive constrained characters is upper bounded by some value, which is called GB-CPSA, we give a dynamic programming with the time complexity O(kn4/ log n). For the constrained centerstar sequence alignment (CCSA), we prove that it is NP-hard to achieve the optimal alignment even over the binary alphabet. Furthermore, we show a negative result for CCSA, i.e., there is no polynomial-time algorithm to approximate the CCSA within any constant ratio. |
| 收录类别 | SCI |
| 原文出处 | http://link.springer.com/article/10.1007%2Fs10878-015-9914-6 |
| 语种 | 英语 |
| 源URL | [http://ir.siat.ac.cn:8080/handle/172644/10193]  |
| 专题 | 深圳先进技术研究院_数字所 |
| 作者单位 | Journal of Combinatorial Optimization |
| 推荐引用方式 GB/T 7714 | Yong Zhang,Joseph Wun-Tat Chan,Francis Y. L. Chin,et al. Constrained Pairwise and Center-Star Sequences Alignment Problems[J]. Journal of Combinatorial Optimization,2016. |
| APA | Yong Zhang.,Joseph Wun-Tat Chan.,Francis Y. L. Chin.,Hing-Fung Ting.,Deshi Ye.,...&Jianyu Shi.(2016).Constrained Pairwise and Center-Star Sequences Alignment Problems.Journal of Combinatorial Optimization. |
| MLA | Yong Zhang,et al."Constrained Pairwise and Center-Star Sequences Alignment Problems".Journal of Combinatorial Optimization (2016). |
入库方式： OAI收割
来源：深圳先进技术研究院
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