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A symmetry-inclusive algebraic approach to genome rearrangement

Citation

Terauds, V and Stevenson, J and Sumner, J, A symmetry-inclusive algebraic approach to genome rearrangement, Journal of Bioinformatics and Computational Biology, 19, (6) Article 2140015. ISSN 0219-7200 (2021) [Refereed Article]

Copyright Statement

Copyright 2021 World Scientific Publishing Europe Ltd.

DOI: doi:10.1142/S0219720021400151

Abstract

Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position paradigm", in which genomes are represented as permutations signifying the position (and orientation) of each region, enables a refined model-based approach, where one can select biologically plausible rearrangements and assign to them relative probabilities/costs. Here, one must further incorporate any underlying structural symmetry of the genomes into the calculations and ensure that this symmetry is reflected in the model. In our recently-introduced framework of {\em genome algebras}, each genome corresponds to an element that simultaneously incorporates all of its inherent physical symmetries. The representation theory of these algebras then provides a natural model of evolution via rearrangement as a Markov chain. Whilst the implementation of this framework to calculate distances for genomes with `practical' numbers of regions is currently computationally infeasible, we consider it to be a significant theoretical advance: one can incorporate different genomic modelling assumptions, calculate various genomic distances, and compare the results under different rearrangement models. The aim of this paper is to demonstrate some of these features.

Item Details

Item Type:Refereed Article
Keywords:genome rearrangement models, genome symmetry, evolutionary distance, representation theory
Research Division:Mathematical Sciences
Research Group:Applied mathematics
Research Field:Biological mathematics
Objective Division:Expanding Knowledge
Objective Group:Expanding knowledge
Objective Field:Expanding knowledge in the mathematical sciences
UTAS Author:Terauds, V (Dr Venta Terauds)
UTAS Author:Stevenson, J (Mr Joshua Stevenson)
UTAS Author:Sumner, J (Associate Professor Jeremy Sumner)
ID Code:149479
Year Published:2021
Web of Science® Times Cited:2
Deposited By:Mathematics
Deposited On:2022-04-01
Last Modified:2022-05-04
Downloads:0

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