Acta Mathematicae Applicatae Sinica

, Volume 22, Issue 3, pp 405–412

A Dynamic Programming Algorithm for the k-Haplotyping Problem

  • Zhen-ping Li
  • Ling-yun Wu
  • Yu-ying Zhao
  • Xiang-sun Zhang
Original Papers

DOI: 10.1007/s10255-006-0315-6

Cite this article as:
Li, Z., Wu, L., Zhao, Y. et al. Acta Math. Appl. Sin, Engl. Ser. (2006) 22: 405. doi:10.1007/s10255-006-0315-6

Abstract

The Minimum Fragments Removal (MFR) problem is one of the haplotyping problems: given a set of fragments, remove the minimum number of fragments so that the resulting fragments can be partitioned into k classes of non-conflicting subsets. In this paper, we formulate the k-MFR problem as an integer linear programming problem, and develop a dynamic programming approach to solve the k-MFR problem for both the gapless and gap cases.

Keywords

Integer programming dynamic programming k-haplotyping SNP 

2000 MR Subject Classification

90C39 90C90 92C40 

Copyright information

© Springer-Verlag Berlin Heidelberg 2006

Authors and Affiliations

  • Zhen-ping Li
    • 1
    • 2
  • Ling-yun Wu
    • 1
  • Yu-ying Zhao
    • 3
  • Xiang-sun Zhang
    • 1
  1. 1.Institute of Applied MathematicsAcademy of Mathematics and Systems Science, CASBeijingChina
  2. 2.Mathematics Department of BeijingWuzi UniversityBeijingChina
  3. 3.Mathematics Department of Beijing Forest UniversityBeijingChina

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