A parameterized enumeration algorithm for the haplotype assembly problem

Abstract

Given DNA sequence fragments from a pair of chromosomes, the goal of the haplotype assembly problem is to reconstruct the two haplotypes of the underlying chromosomes. Many heuristic algorithms and exact algorithms have been introduced for the problem, and they aim to reconstruct a pair of haplotypes that is optimal or near-optimal. However given an input fragments data the optimal solution may be not unique, but these algorithms can only choose one randomly or the one they find at first. This paper proposes a parameterized enumeration algorithm for the Minimum Single Nucleotide Polymorphism (SNP) Removal model of the problem. Extensive experiments show that the algorithm can effectively provide multiple optimal solutions to biologists for further analyses.