Department of Computer Engineering, University of Zanjan, Zanjan, Iran.
Comput Biol Chem. 2018 Feb;72:1-10. doi: 10.1016/j.compbiolchem.2017.12.005. Epub 2017 Dec 14.
In this paper, a method for single individual haplotype (SIH) reconstruction using Asexual reproduction optimization (ARO) is proposed. Haplotypes, as a set of genetic variations in each chromosome, contain vital information such as the relationship between human genome and diseases. Finding haplotypes in diploid organisms is a challenging task. Experimental methods are expensive and require special equipment. In SIH problem, we encounter with several fragments and each fragment covers some parts of desired haplotype. The main goal is bi-partitioning of the fragments with minimum error correction (MEC). This problem is addressed as NP-hard and several attempts have been made in order to solve it using heuristic methods. The current method, AROHap, has two main phases. In the first phase, most of the fragments are clustered based on a practical metric distance. In the second phase, ARO algorithm as a fast convergence bio-inspired method is used to improve the initial bi-partitioning of the fragments in the previous step. AROHap is implemented with several benchmark datasets. The experimental results demonstrate that satisfactory results were obtained, proving that AROHap can be used for SIH reconstruction problem.
本文提出了一种使用无性繁殖优化（ARO）进行单体单倍型（SIH）重建的方法。单倍型作为每条染色体上的一组遗传变异，包含了人类基因组与疾病之间关系等重要信息。在二倍体生物中寻找单倍型是一项具有挑战性的任务。实验方法昂贵且需要特殊设备。在 SIH 问题中，我们会遇到多个片段，每个片段都覆盖了所需单倍型的某些部分。主要目标是通过最小错误校正（MEC）将片段进行二分。这个问题被认为是 NP 难的，已经有一些尝试使用启发式方法来解决它。当前的方法 AROHap 有两个主要阶段。在第一阶段，根据实际的度量距离对大多数片段进行聚类。在第二阶段，使用快速收敛的生物启发式方法 ARO 算法来改进上一步中片段的初始二分。AROHap 是在几个基准数据集上实现的。实验结果表明，得到了令人满意的结果，证明了 AROHap 可以用于 SIH 重建问题。
