ArticleBMC bioinformatics2015
Moments of genome evolution by Double Cut-and-Join.
Article in BMC bioinformatics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- On the rank-distance median of 3 permutations.BMC bioinformatics · 2018Article
- Genome rearrangements with indels in intergenes restrict the scenario space.BMC bioinformatics · 2016Article
- Breaking Good: Accounting for Fragility of Genomic Regions in Rearrangement Distance Estimation.Genome biology and evolution · 2016Article
- Ancestral gene synteny reconstruction improves extant species scaffolding.BMC genomics · 2015Article
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Authors and funding
3 authors.
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Abstract
We study statistical estimators of the number of genomic events separating two genomes under a Double Cut-and Join (DCJ) rearrangement model, by a method of moment estimation. We first propose an exact, closed, analytically invertible formula for the expected number of breakpoints after a given number of DCJs. This improves over the heuristic, recursive and computationally slower previously proposed one. Then we explore the analogies of genome evolution by DCJ with evolution of binary sequences under substitutions, permutations under transpositions, and random graphs. Each of these are presented in the literature with intuitive justifications, and are used to import results from better known fields. We formalize the relations by proving a correspondence between moments in sequence and genome evolution, provided substitutions appear four by four in the corresponding model. Eventually we prove a bounded error on two estimators of the number of cycles in the breakpoint graph after a given number of rearrangements, by an analogy with cycles in permutations and components in random graphs.
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