A practical exact algorithm for the individual haplotyping problem MEC/GI

Abstract

Given the genotype and the aligned single nucleotide polymorphism (SNP) fragments of an individual, Minimum Error Correction with Genotype Information (MEC/GI) is an important computational model to infer a pair of haplotypes compatible with the genotype by correcting minimum number of SNPs in the given SNP fragments. For the problem, there has been no practical exact algorithm. In DNA sequencing experiments, due to technical limits, the maximum length of a fragment sequenced directly is about 1kb. In consequence, the maximum number k of SNP sites that a fragment covers is usually small (usually smaller than 10). Based on the observation above, the current paper introduces a new parameterized dynamic programming algorithm of running time O(mk2k + mlogm + mk), where m is the number of fragments. The algorithm solves the MEC/GI problem efficiently even if the number of fragments and SNPs are large, and is practical in real biological applications. © 2008 Springer-Verlag Berlin Heidelberg.