计算机工程与应用 ›› 2010, Vol. 46 ›› Issue (8): 217-220.DOI: 10.3778/j.issn.1002-8331.2010.08.063

• 工程与应用 • 上一篇    下一篇

遗传算法和单体型组装加权最小字符翻转问题

姚雄武,郑金华,李 晶,文诗华   

  1. 湘潭大学 信息工程学院,湖南 湘潭 411105
  • 收稿日期:2008-09-09 修回日期:2008-11-21 出版日期:2010-03-11 发布日期:2010-03-11
  • 通讯作者: 姚雄武

Genetic algorithm and haplotype assembly problem Weighted Minimum Letter Flips

YAO Xiong-wu,ZHENG Jin-hua,LI Jing,WEN Shi-hua   

  1. School of Information Engineering,Xiangtan University,Xiangtan,Hunan 411105,China
  • Received:2008-09-09 Revised:2008-11-21 Online:2010-03-11 Published:2010-03-11
  • Contact: YAO Xiong-wu

摘要: 单体型组装加权最小字符翻转(WMLF)问题指定个体联配的加权DNA片断数据,翻转权值和最小的SNP位点以推测出该个体的一对单体型。该问题是NP-难的,至今尚无实用的搜索寻优算法。根据DNA测序片段数据的特点提出了一种遗传算法。对于实际的生物实验数据,即使数据很大,该算法也可以在较短的时间得到WMLF问题的满意解,具有良好的可扩展性和较高的实用价值。

Abstract: Given a set of weighted aligned DNA fragments of an individual,the haplotype assembly problem Weighted Minimum Letter Flips(WMLF) is to infer a pair of haplotypes of the individual by flipping some SNPs with the sum of weights of the flipped SNPs minimized.WMLF is NP-hard,and there is no practical algorithm to search optimal solution for the problem.Based on the characters of DNA fragments,this paper introduces a genetic algorithm.For the practical fragment data,the algorithm can solve the WMLF problem efficiently even if the data are larger,and it is scalable and applicable in practice.

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