# Bayesian sampling of genomic rearrangement scenarios via double cut and join

@article{Mikls2010BayesianSO, title={Bayesian sampling of genomic rearrangement scenarios via double cut and join}, author={Istv{\'a}n Mikl{\'o}s and {\'E}ric Tannier}, journal={Bioinformatics}, year={2010}, volume={26 24}, pages={ 3012-9 } }

MOTIVATION
When comparing the organization of two genomes, it is important not to draw conclusions on their modes of evolution from a single most parsimonious scenario explaining their differences. Better estimations can be obtained by sampling many different genomic rearrangement scenarios. For this problem, the Double Cut and Join (DCJ) model, while less relevant, is computationally easier than the Hannenhalli-Pevzner (HP) model. Indeed, in some special cases, the total number of DCJ sorting…

## 18 Citations

### Sampling and counting genome rearrangement scenarios

- Computer ScienceBMC Bioinformatics
- 2015

A Gibbs sampler for sampling most parsimonious labeling of evolutionary trees under the SCJ model and a mini-review about the state of the art of sampling and counting rearrangement scenarios, focusing on the reversal, DCJ and SCJ models are given.

### Approximating the number of Double Cut-and-Join scenarios

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### Maximum likelihood estimates of pairwise rearrangement distances.

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### Calibration of a probabilistic model of DNA evolution

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This thesis describes a model of evolution where the DNA is represented by genes, and it describes how optimal parameters for this model can be found, and the main focus lies on the estimation of the number of chromosomal events.

### Algorithms and methods for large-scale genome rearrangements identification

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This thesis by compendium addresses the formal definition of SB starting from High-Scoring Segments Pairs (HSPs), and provides a solution for the granularity problem in the SB detection: starting with small and well-conserved SB and through rearrangement reconstruction gradually increasing the length of the SB.

### Variants of the Consecutive Ones Property: Algorithms, Computational Complexity and Applications to Genomics

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It is shown that the problem of optimizing over the set of repeat spanning intervals is NP-hard in general, and given an algorithm when the intervals are small.

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- BiologyBioinform.
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This work analyzes 15 vertebrate genomes, including 12 amniotes and 3 teleost fishes, and infer a high-resolution genome organization of the amniote ancestral genome, composed of 39 ancestral linkage groups at a resolution of 100 kb, and shows that 36 out of 39 have maximum support.

### Linearization of ancestral multichromosomal genomes

- BiologyBMC Bioinformatics
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This work shows that, when restricted to binary matrices of degree two, which correspond to adjacencies, the genomic characters used in most ancestral genome reconstruction methods, this relaxed version of the Linearization Problem is polynomially solvable using a reduction to a matching problem.

### The Inference of Gene Trees with Species Trees

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Simulations as well as empirical studies on genomic data show that combining gene tree–species tree models with models of sequence evolution improves gene tree reconstruction, and these better gene trees provide a more reliable basis for studying genome evolution or reconstructing ancestral chromosomes and ancestral gene sequences.

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