Haplotyping a single triploid individual based on genetic algorithm

Abstract

The minimum error correction model is an important combinatorial model for haplotyping a single individual. In this article, triploid individual haplotype reconstruction problem is studied by using the model. A genetic algorithm based method GTIHR is presented for reconstructing the triploid individual haplotype. A novel coding method and an effectual hillclimbing operator are introduced for the GTIHR algorithm. This relatively short chromosome code can lead to a smaller solution space, which plays a positive role in speeding up the convergence process. The hill-climbing operator ensures algorithm GTIHR converge at a good solution quickly, and prevents premature convergence simultaneously. The experimental results prove that algorithm GTIHR can be implemented efficiently, and can get higher reconstruction rate than previous algorithms.

A fast and accurate enumeration-based algorithm for haplotyping a triploid individual

“…It can obtain better performance than the HapCompass algorithm [ 13 ]. In 2014, based on the MEC model, Wu et al [ 14 ] presented a genetic algorithm GTIHR for reconstructing triploid haplotypes. Since the code length of algorithm GTIHR equals to the number of heterozygous sites in haplotype, the performance of the GTIHR algorithm is negatively affected by haplotype length and heterozygous rate.…”