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Position and Content Paradigms in Genome Rearrangements: The Wild and Crazy World of Permutations in Genomics

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Abstract

Modellers of large-scale genome rearrangement events, in which segments of DNA are inverted, moved, swapped, or even inserted or deleted, have found a natural syntax in the language of permutations. Despite this, there has been a wide range of modelling choices, assumptions and interpretations that make navigating the literature a significant challenge. Indeed, even authors of papers that use permutations to model genome rearrangement can struggle to interpret each others’ work, because of subtle differences in basic assumptions that are often deeply ingrained (and consequently sometimes not even mentioned). In this paper, we describe the different ways in which permutations have been used to model genomes and genome rearrangement events, presenting some features and limitations of each approach, and show how the various models are related. This paper will help researchers navigate the landscape of permutation-based genome rearrangement models and make it easier for authors to present clear and consistent models.

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Acknowledgements

This research was partly undertaken during reciprocal visits of PF to Western Sydney University and ARF to Bielefeld University. The authors acknowledge the support of these institutions.

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Author notes

  1. Sangeeta Bhatia

    Present address: School of Public Health, Imperial College, London, UK

Authors and Affiliations

  1. Centre for Research in Mathematics, Western Sydney University, Sydney, Australia

    Sangeeta Bhatia & Andrew R. Francis

  2. Faculty of Technology, Universität Bielefeld, Bielefeld, Germany

    Pedro Feijão

Authors
  1. Sangeeta Bhatia
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  2. Pedro Feijão
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  3. Andrew R. Francis
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Corresponding author

Correspondence to Sangeeta Bhatia.

Additional information

Research supported in part by Australian Research Council Discovery Grant DP130100248.

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Bhatia, S., Feijão, P. & Francis, A.R. Position and Content Paradigms in Genome Rearrangements: The Wild and Crazy World of Permutations in Genomics. Bull Math Biol 80, 3227–3246 (2018). https://doi.org/10.1007/s11538-018-0514-3

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