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A symmetry-inclusive algebraic approach to genome rearrangement

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dc.contributor.authorTerauds, V.
dc.contributor.authorStevenson, J.
dc.contributor.authorSumner, J.
dc.date.issued2021
dc.descriptionLink to a related website: https://unpaywall.org/10.1142/s0219720021400151, Open Access via Unpaywall
dc.description.abstractOf the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modeling 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 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 modeling 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.
dc.identifier.citationJournal of Bioinformatics and Computational Biology, 2021; 19(6):1-18
dc.identifier.doi10.1142/s0219720021400151
dc.identifier.issn0219-7200
dc.identifier.issn1757-6334
dc.identifier.urihttps://hdl.handle.net/11541.2/36093
dc.language.isoen
dc.publisherWorld Scientific Publishing Europe Ltd.
dc.relation.fundingARC DP180102215
dc.relation.fundingARDC
dc.rightsCopyright 2021 World Scientific Publishing Europe Ltd.
dc.source.urihttps://doi.org/10.1142/s0219720021400151
dc.subjectgenome rearrangement models
dc.subjectgenome symmetry
dc.subjectevolutionary distance
dc.subjectrepresentation theory
dc.titleA symmetry-inclusive algebraic approach to genome rearrangement
dc.typeJournal article
pubs.publication-statusPublished
ror.mmsid9916800027401831

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