Computer Engineering and Applications ›› 2010, Vol. 46 ›› Issue (8): 217-220.DOI: 10.3778/j.issn.1002-8331.2010.08.063
• 工程与应用 • Previous Articles Next Articles
YAO Xiong-wu,ZHENG Jin-hua,LI Jing,WEN Shi-hua
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姚雄武,郑金华,李 晶,文诗华
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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.
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。
CLC Number:
TP18
YAO Xiong-wu,ZHENG Jin-hua,LI Jing,WEN Shi-hua. Genetic algorithm and haplotype assembly problem Weighted Minimum Letter Flips[J]. Computer Engineering and Applications, 2010, 46(8): 217-220.
姚雄武,郑金华,李 晶,文诗华. 遗传算法和单体型组装加权最小字符翻转问题[J]. 计算机工程与应用, 2010, 46(8): 217-220.
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URL: http://cea.ceaj.org/EN/10.3778/j.issn.1002-8331.2010.08.063
http://cea.ceaj.org/EN/Y2010/V46/I8/217