An Extension of Heuristic Algorithm for Reconstructing Multiple Haplotypes with Minimum Error Correction

Abstract

Human DNA consists of two copies of each chromosome. The haplotype assembly problem focuses on the reconstruction of two sets of haplotypes (chromosomes) from aligned fragments of the genome sequence. Plants like rice, wheat, and banana consist of more than two chromosomes which mean multiple haplotypes. Reconstructing multiple haplotypes has become an intense research interest. There are several models that have been developed for the reconstruction of multiple haplotypes from a polyploid genome. The computational challenge still attracts researchers. We are extending the heuristic algorithm for individual haplotyping in order to reconstruct multiple haplotypes for a polyploid organism so that the number of errors among the groups of DNA reads is minimum. We are using a metric that determines the read or fragment which fits for none of the constructed groups and it results in the creation of a new group. Experimental results on real and simulated data and their comparison with existing models show that our model can reconstruct multiple groups with less computational time and memory usage.