A parsimonious tree-grow method for haplotype inference.

Zhenping Li; Wenfeng Zhou; Xiang-Sun Zhang; Luonan Chen

doi:10.1093/bioinformatics/bti572

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A parsimonious tree-grow method for haplotype inference.

Zhenping Li·Wenfeng Zhou·Xiang-Sun Zhang·Luonan Chen

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Abstract

MOTIVATION: Haplotype information has become increasingly important in analyzing fine-scale molecular genetics data, such as disease genes mapping and drug design. Parsimony haplotyping is one of haplotyping problems belonging to NP-hard class. RESULTS: In this paper, we aim to develop a novel algorithm for the haplotype inference problem with the parsimony criterion, based on a parsimonious tree-grow method (PTG). PTG is a heuristic algorithm that can find the minimum number of distinct haplotypes based on the criterion of keeping all genotypes resolved during tree-grow process. In addition, a block-partitioning method is also proposed to improve the computational efficiency. We show that the proposed approach is not only effective with a high accuracy, but also very efficient with the computational complexity in the order of O(m2n) time for n single nucleotide polymorphism sites in m individual genotypes. AVAILABILITY: The software is available upon request from the authors, or from http://zhangroup.aporc.org/bioinfo/ptg/ CONTACT: chen@elec.osaka-sandai.ac.jp SUPPLEMENTARY INFORMATION: Supporting materials is available from http://zhangroup.aporc.org/bioinfo/ptg/bti572supplementary.pdf

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Algorithms Base Sequence Chromosome Mapping Haplotypes Models, Genetic Molecular Sequence Data Phenotype Polymorphism, Single Nucleotide Sequence Alignment Sequence Analysis, DNA Software Evaluation Study Journal Article Research Support, Non-U.S. Gov't

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Zhenping Li, Wenfeng Zhou, Xiang-Sun Zhang, Luonan Chen. 2005-07-07. A parsimonious tree-grow method for haplotype inference.. https://doi.org/10.1093/bioinformatics%2Fbti572

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