A parthenogenetic algorithm for single individual SNP haplotyping

The minimum error correction (MEC) model is one of the important computational models for single individual single nucleotide polymorphism (SNP) haplotyping. Due to the NP-hardness of the model, Qian et al. presented a particle swarm optimization (PSO) algorithm to solve it, and the particle code length is equal to the number of SNP fragments. However, there are hundreds and thousands of SNP fragments in practical applications. The PSO algorithm based on this kind of long particle code cannot obtain high reconstruction rate efficiently. In this paper, a practical heuristic algorithm PGA-MEC based on parthenogenetic algorithm (PGA) is presented to solve the model. A kind of short chromosome code and an effective recombination operator are designed for the algorithm. The reconstruction rate of PGA-MEC algorithm is higher than that of PSO algorithm and the running time of PGA-MEC algorithm is shorter than that of PSO algorithm, which are proved by a number of experiments.