A Path-Deformation Framework for Determining Weighted Genome Rearrangement Distance
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 sh...
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| Vydáno v: | Frontiers in genetics Ročník 11; s. 1035 |
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| Hlavní autoři: | , , , , , |
| Médium: | Journal Article |
| Jazyk: | angličtina |
| Vydáno: |
Frontiers Media S.A
24.09.2020
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| Témata: | |
| ISSN: | 1664-8021, 1664-8021 |
| On-line přístup: | Získat plný text |
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| Shrnutí: | 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.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. |
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| Bibliografie: | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Present address: Sangeeta Bhatia, MRC Center for Global Infectious Disease Analysis, School of Public Health, Imperial College London, London, United Kingdom Edited by: Ruriko Yoshida, Naval Postgraduate School, United States This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Genetics Attila Egri-Nagy, Akita International University, Akita, Japan Reviewed by: David Murrugarra, University of Kentucky, United States; Xiaoxian Tang, Beihang University, China |
| ISSN: | 1664-8021 1664-8021 |
| DOI: | 10.3389/fgene.2020.01035 |