枚举有符号基因组的可行交互移位算法
收稿日期: 2010-03-03
修回日期: 2010-06-14
网络出版日期: 2010-09-02
基金资助
国家自然科学基金资助项目(60970003)
An Algorithm of Reciprocal Translocationsfor Enumerating Signed Genomes
Received date: 2010-03-03
Revised date: 2010-06-14
Online published: 2010-09-02
交互移位排序问题(SRT)是寻找一个使一个基因组转变为另一个基因组的最短交互移位序列。现在已有多个多项式时间的SRT算法,但大多数问题实例都有许多个最短交互移位序列,因此寻找所有最短交互移位序列问题是SRT一个自然的推广。这个问题可以归约为寻找一个基因组相对于另一个基因组的全部可行交互移位,即所有移位ρ满足:在一个基因组上执行ρ之后,所得基因组相对于另一个基因组的移位距离会减少。本文提出一个用来寻找全部可行交互移位的有效算法,尽管新算法的时间复杂度比穷举法改进不大,但实验结果表明,其在实际运行中表现更好。
关键词: 基因组重组;交互移位排序;移位距离
陈超,栾峻峰 . 枚举有符号基因组的可行交互移位算法[J]. 计算机工程与科学, 2010 , 32(9) : 152 -156 . DOI: 10.3969/j.issn.1007130X.2010.
During the past decades,several polynomial algorithms have been developed for the problem of sorting by reciprocal translocations (abbreviated as SRT), which is to find the shortest sequence of reciprocal translocations that transforms one genome into another. However, there are many shortest sequences of reciprocal translocations for most problem instances. In consequence, the problem of finding all the shortest sequences of reciprocal translocations is a natural generalization of SRT. This problem reduces easily to the problem of finding all the “sorting reciprocal translocations” of one genome with respect to another—that is, all translocations ρ which can reduce the translocation distance of the resulting genome from another after applying ρ on one genome. In this paper, we give an efficient algorithm for finding all the sorting reciprocal translocations. While the new algorithm improves little in asymptotic time complexity, the experimental results show that it performs better in practice than the brute force method.
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