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Haplotype assembly from aligned weighted SNP fragments �
| Citations: | 9 - 0 self |
BibTeX
@MISC{Zhao_haplotypeassembly,
author = {Yu-ying Zhao and Ling-yun Wu and Ji-hong Zhang and Rui-sheng Wang and Xiang-sun Zhang},
title = {Haplotype assembly from aligned weighted SNP fragments �},
year = {}
}
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Abstract
Given an assembled genome of a diploid organism the haplotype assembly problem can be formulated as retrieval of a pair of haplotypes from a set of aligned weighted SNP fragments. Known computational formulations (models) of this problem are minimum letter flips (MLF) and the weighted minimum letter flips (WMLF; Greenberg et al. (INFORMS J. Comput. 2004, 14, 211–213)). In this paper we show that the general WMLF model is NP-hard even for the gapless case. However the algorithmic solutions for selected variants of WMFL can exist and we propose a heuristic algorithm based on a dynamic clustering technique. We also introduce a new formulation of the haplotype assembly problem that we call COMPLETE WMLF (CWMLF). This model and algorithms for its implementation take into account a simultaneous presence of multiple kinds of data errors. Extensive computational experiments indicate that the algorithmic implementations of the CWMLF model achieve higher accuracy of haplotype reconstruction than the WMLF-based algorithms, which in turn appear to be more accurate than those based on MLF.
Keyphrases
weighted snp fragment haplotype assembly haplotype assembly problem simultaneous presence complete wmlf data error general wmlf model new formulation known computational formulation multiple kind aligned weighted snp fragment assembled genome cwmlf model achieve haplotype reconstruction algorithmic solution algorithmic implementation minimum letter flip extensive computational experiment gapless case diploid organism dynamic clustering technique wmlf-based algorithm heuristic algorithm weighted minimum letter flip
