# Counting All DCJ Sorting Scenarios

@inproceedings{Braga2009CountingAD, title={Counting All DCJ Sorting Scenarios}, author={Mar{\'i}lia Dias Vieira Braga and Jens Stoye}, booktitle={RECOMB-CG}, year={2009} }

In genome rearrangements, the double cut and join (DCJ) operation, introduced by Yancopoulos et al. , allows to represent most rearrangement events that could happen in multichromosomal genomes, such as inversions, translocations, fusions and fissions. No restriction on the genome structure considering linear and circular chromosomes is imposed. An advantage of this general model is that it leads to considerable algorithmic simplifications. Recently several works concerning the DCJ operation…

## 14 Citations

### The Solution Space of Sorting by DCJ

- BiologyJ. Comput. Biol.
- 2010

An easy-to-compute formula is given that corresponds to the exact number of optimal DCJ sorting sequences for a particular subset of instances of the problem and the demonstration of the possibility of obtaining one optimal sorting sequence by properly replacing any pair of consecutive operations in another optimal sequence.

### All Possible Optimal Solutions for Multichromosomal Genome Rearrangements using DCJ

- Biology
- 2015

The whole space of solutions for this problem and some propositions are given, on the basis of which a theoretical algorithm has been proposed, to find one optimal DCJ rearrangement sequence for sorting one genome into the another one.

### Algebraic double cut and join

- BiologyJournal of mathematical biology
- 2015

This paper realizes the double cut and join operator as a group action on the space of multichromosomal genomes, deriving some properties of the group and finding group-theoretic analogues for the key results in the DCJ theory.

### Visualization of genome rearrangements using DCJ operations

- BiologyIWISC
- 2018

A novel visualization program is introduced, DCJVis, to create a diagram of each DCJ operations necessary to transform between the genomes of two distinct organisms by describing a possible sequence of genome graphs based on the selected gene adjacency for the DCJ operation.

### ALGEBRAIC MODELS OF LARGE SCALE GENOME REARRANGEMENT EVENTS

- BiologyBulletin of the Australian Mathematical Society
- 2019

This work is the first to apply the theory of rewriting systems to a problem in phylogenetics, thereby linking these two separate fields and contributing to the conversation between algebra and biology.

### DCJVis: visualization of genome rearrangements using DCJ operations

- Biology
- 2017

A new visualization program is introduced, DCJVis, to create a diagram of each DCJ operation necessary to transform between the genomes of two distinct organisms by describing a possible sequence of genome graphs based on the selected gene adjacency on the source genome for theDCJ operation.

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

- Computer ScienceBioinform.
- 2010

Two theorems underlying the theoretical mixing properties of the Double Cut and Join model are introduced, based on a parallel MCMC method that cools down DCJ scenarios to HP scenarios, and allowed us to provide estimates of the different modes of evolution in diverse lineages.

### 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.

### Phylogenetic Reconstruction Analysis on Gene Order and Copy Number Variation

- Biology
- 2019

A new median solver for gene order data that combines double-cut-join (DCJ) sorting with the Simulated Annealing algorithm (SAMedian) is proposed and a new phylogenetic inference method is built to solve both SPP and BPP problems.

### Gene order rearrangement methods for the reconstruction of phylogeny

- Biology
- 2009

Two fundamental genome rearrangement problems are studied in this thesis and it is shown that increased plausibility can be accompanied by an efficient solution.

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