Finding all maximal perfect haplotype blocks in linear time

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

Research output: Chapter in Book/Report/Conference proceedingConference contribution

2 Citations (Scopus)

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.

Original languageEnglish
Title of host publication19th International Workshop on Algorithms in Bioinformatics, WABI 2019
EditorsKatharina T. Huber, Dan Gusfield
PublisherSchloss Dagstuhl- Leibniz-Zentrum fur Informatik GmbH, Dagstuhl Publishing
ISBN (Electronic)9783959771238
DOIs
Publication statusPublished - Sep 2019
Event19th International Workshop on Algorithms in Bioinformatics, WABI 2019 - Niagara Falls, United States
Duration: Sep 8 2019Sep 10 2019

Publication series

NameLeibniz International Proceedings in Informatics, LIPIcs
Volume143
ISSN (Print)1868-8969

Conference

Conference19th International Workshop on Algorithms in Bioinformatics, WABI 2019
CountryUnited States
CityNiagara Falls
Period9/8/199/10/19

All Science Journal Classification (ASJC) codes

  • Software

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