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A symmetry-inclusive algebraic approach to genome rearrangement

Terauds, V ORCID: 0000-0002-6891-5333, Stevenson, J ORCID: 0000-0002-1037-9996 and Sumner, J ORCID: 0000-0001-9820-0235 2021 , 'A symmetry-inclusive algebraic approach to genome rearrangement' , Journal of Bioinformatics and Computational Biology, vol. 19, no. 6 , doi: 10.1142/S0219720021400151.

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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 Type: Article
Authors/Creators:Terauds, V and Stevenson, J and Sumner, J
Keywords: genome rearrangement models, genome symmetry, evolutionary distance, representation theory
Journal or Publication Title: Journal of Bioinformatics and Computational Biology
Publisher: World Scientific Publishing Europe Ltd.
ISSN: 0219-7200
DOI / ID Number: 10.1142/S0219720021400151
Copyright Information:

Copyright 2021 World Scientific Publishing Europe Ltd.

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