A Path-Deformation Framework for Determining Weighted Genome Rearrangement Distance.

Sangeeta Bhatia, Attila Egri-Nagy, Stuart Serdoz, Cheryl E Praeger, Volker Gebhardt, Andrew Francis

Abstract read

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Article in Frontiers in genetics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

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1citing papers in PubMed

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1 citing paper in PubMed.

A mean first passage time genome rearrangement distance.Journal of mathematical biology · 2020
Article

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5 · Who and what money

Authors and funding

6 authors.

Sangeeta BhatiaCentre for Research in Mathematics and Data Science, Western Sydney University, Sydney, NSW, Australia.

Attila Egri-NagyCentre for Research in Mathematics and Data Science, Western Sydney University, Sydney, NSW, Australia.

Stuart SerdozCentre for Research in Mathematics and Data Science, Western Sydney University, Sydney, NSW, Australia.

Cheryl E PraegerSchool of Physics, Mathematics, and Computing, University of Western Australia, Perth, WA, Australia.

Volker GebhardtCentre for Research in Mathematics and Data Science, Western Sydney University, Sydney, NSW, Australia.

Andrew FrancisCentre for Research in Mathematics and Data Science, Western Sydney University, Sydney, NSW, Australia.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Measuring the distance between two bacterial genomes under the inversion process is usually done by assuming all inversions to occur with equal probability. Recently, an approach to calculating inversion distance using group theory was introduced, and is effective for the model in which only very short inversions occur. In this paper, we show how to use the group-theoretic framework to establish minimal distance for any weighting on the set of inversions, generalizing previous approaches. To do this we use the theory of rewriting systems for groups, and exploit the Knuth-Bendix algorithm, the first time this theory has been introduced into genome rearrangement problems. The central idea of the approach is to use existing group theoretic methods to find an initial path between two genomes in genome space (for instance using only short inversions), and then to deform this path to optimality using a confluent system of rewriting rules generated by the Knuth-Bendix algorithm.

Indexed as

genome rearrangementgroup theoryinversionKnuth-Bendix algorithmrewriting systems

Identifiers

PMID33193592

DOI10.3389/fgene.2020.01035

PMCPMC7542183

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