Finding all maximal perfect haplotype blocks in linear time

Jarno Alanko, Hideo Bannai, Bastien Cazaux, Pierre Peterlongo, Jens Stoye

研究成果: Contribution to journalArticle査読

3 被引用数 (Scopus)

抄録

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. (Advances in bioinformatics and computational biology: 11th Brazilian symposium on bioinformatics, BSB 2018, Niterói, Brazil, October 30 - November 1, 2018, Proceedings, 2018. https://doi.org/10.1007/978-3-030-01722-4_3) 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.

本文言語英語
論文番号2
ジャーナルAlgorithms for Molecular Biology
15
1
DOI
出版ステータス出版済み - 2 10 2020

All Science Journal Classification (ASJC) codes

  • 構造生物学
  • 分子生物学
  • 計算理論と計算数学
  • 応用数学

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