A new paradigm for identifying reconciliation-scenario altering mutations conferring environmental adaptation

Research output: Chapter in Book/Report/Conference proceedingConference contributionpeer-review

Abstract

An important goal in microbial computational genomics is to identify crucial events in the evolution of a gene that severely alter the duplication, loss and mobilization patterns of the gene within the genomes in which it disseminates. In this paper, we formalize this microbiological goal as a new pattern-matching problem in the domain of Gene tree and Species tree reconciliation, denoted “Reconciliation-Scenario Altering Mutation (RSAM) Discovery”. We propose an O(m · n · k) time algorithm to solve this new problem, where m and n are the number of vertices of the input Gene tree and Species tree, respectively, and k is a user-specified parameter that bounds from above the number of optimal solutions of interest. The algorithm first constructs a hypergraph representing the k highest scoring reconciliation scenarios between the given Gene tree and Species tree, and then interrogates this hypergraph for subtrees matching a pre-specified RSAM Pattern. Our algorithm is optimal in the sense that the number of hypernodes in the hypergraph can be lower bounded by Ω(m · n · k). We implement the new algorithm as a tool, denoted RSAM-finder, and demonstrate its application to the identification of RSAMs in toxins and drug resistance elements across a dataset spanning hundreds of species.

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
StatePublished - 1 Sep 2019
Event19th International Workshop on Algorithms in Bioinformatics, WABI 2019 - Niagara Falls, United States
Duration: 8 Sep 201910 Sep 2019

Publication series

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

Conference

Conference19th International Workshop on Algorithms in Bioinformatics, WABI 2019
Country/TerritoryUnited States
CityNiagara Falls
Period8/09/1910/09/19

Keywords

  • Gene tree
  • Reconciliation
  • Species tree

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