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针对最少错误更正(the minimum error correction,MEC)模型,对三倍体个体单体型重建问题进行研究,提出一种基于遗传算法的三倍体个体单体型重建算法GTIHR.该算法采用一种新颖的染色体编码方法和一种有效的爬山算子.这种较短的染色体编码方式能够构造较小的解空间,以便于算法快速收敛到较优解.此外,爬山算子通过为染色体编码注入随机信息来避免早熟现象,并充分利用SNP片段中的有效信息来逐步修正染色体编码取值.实验利用鸟枪法测序模拟片段生成器CELSIM生成片段数据.与以往求解算法的比较分析结果显示,GTIHR算法能够获得更高重建率的单体型,具有较强的实用价值.
Aiming at the minimum error correction (MEC) model, this paper studies the haplotypic reconstruction of triploid individuals and proposes a GTIHR algorithm based on genetic algorithm to reconstruct the haplotypic haplotypes. The algorithm uses a A novel chromosome coding method and an effective hill climbing operator.The shorter chromosome coding method can construct a smaller solution space so that the algorithm can quickly converge to an optimal solution.In addition, Random information to avoid premature phenomenon, and make full use of valid information in SNP fragments to gradually correct the chromosome coding values.Combined with shotgun sequencing experiments using fragment generator CELSIM generated fragment data.Compared with the previous solution algorithm analysis results show that GTIHR algorithm Can get a higher reconstruction rate of haplotype, with strong practical value.