Technical comment: A clustering algorithm based on two distance functions for MEC model

Authors:
Ying Wang;Enmin Feng;Ruisheng Wang
Affiliations:
Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, China;Department of Applied Mathematics, Dalian University of Technology, Dalian 116024, China;School of Information, Renmin University of China, Beijing 100872, China
Venue:
Computational Biology and Chemistry
Year:
2007

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Abstract

Haplotype reconstruction, based on aligned single nucleotide polymorphism (SNP) fragments, is to infer a pair of haplotypes from localized polymorphism data gathered through short genome fragment assembly. This paper first presents two distance functions, which are used to measure the difference degree and similarity degree between SNP fragments. Based on the two distance functions, a clustering algorithm is proposed in order to solve MEC model. The algorithm involves two sections. One is to determine the initial haplotype pair, the other concerns with inferring true haplotype pair by re-clustering. The comparison results prove that our algorithm utilizing two distance functions is effective and feasible.