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Finding all maximal perfect haplotype blocks in linear time

Abstract : Recent large-scale community sequencing efforts allow at an unprecedented level of detail the identification of genomic regions that show signatures of natural selection. Traditional methods for identifying such regions from individuals' haplotype data, however, require excessive computing times and therefore are not applicable to current datasets. In 2019, Cunha et al. (Proceedings of BSB 2019) suggested the maximal perfect haplotype block as a very simple combinatorial pattern, forming the basis of a new method to perform rapid genome-wide selection scans. The algorithm they presented for identifying these blocks, however, had a worst-case running time quadratic in the genome length. It was posed as an open problem whether an optimal, linear-time algorithm exists. In this paper we give two algorithms that achieve this time bound, one conceptually very simple one using suffix trees and a second one using the positional Burrows-Wheeler Transform, that is very efficient also in practice.
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Contributor : Pierre Peterlongo <>
Submitted on : Wednesday, July 17, 2019 - 4:48:22 PM
Last modification on : Thursday, January 7, 2021 - 4:35:11 PM


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  • HAL Id : hal-02187246, version 1


Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye. Finding all maximal perfect haplotype blocks in linear time. WABI 2019 - Workshop on Algorithms in Bioinformatics, Sep 2019, Niagara Falls, United States. pp.1-9. ⟨hal-02187246⟩



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