Related papers: DCJVis: visualization of genome rearrangements usi…
Establishing a distance between genomes is a significant problem in computational genomics, because its solution can be used to establish evolutionary relationships including phylogeny. The "double cut and join" (DCJ) model of chromosomal…
The inversion distance, that is the distance between two unichromosomal genomes with the same content allowing only inversions of DNA segments, can be exactly computed thanks to a pioneering approach of Hannenhalli and Pevzner from 1995. In…
A "genome structure" is a labeled directed graph with vertices of degree 1 or 2. A set of operations over such graphs is fixed, and each of the operations has a certain cost, a strictly positive number. The transformation problem consists…
Early literature on genome rearrangement modelling views the problem of computing evolutionary distances as an inherently combinatorial one. In particular, attention was given to estimating distances using the minimum number of events…
In this work, we explore heuristics for the Adjacency Graph Packing problem, which can be applied to the Double Cut and Join (DCJ) Distance Problem. The DCJ is a rearrangement operation and the distance problem considering it is a well…
In this paper, we study the problem of sorting unichromosomal linear genomes by prefix double-cut-and-joins (or DCJs) in both the signed and the unsigned settings. Prefix DCJs cut the leftmost segment of a genome and any other segment, and…
In comparative genomics, the rearrangement distance between two genomes (equal the minimal number of genome rearrangements required to transform them into a single genome) is often used for measuring their evolutionary remoteness.…
A classical problem in comparative genomics is to compute the rearrangement distance, that is the minimum number of large-scale rearrangements required to transform a given genome into another given genome. While the most traditional…
The computation of genomic distances has been a very active field of computational comparative genomics over the last 25 years. Substantial results include the polynomial-time computability of the inversion distance by Hannenhalli and…
The circular median problem in the Double-Cut-and-Join (DCJ) distance asks to find, for three given genomes, a fourth circular genome that minimizes the sum of the mutual distances with the three other ones. This problem has been shown to…
We investigate the symmetry of circular genome rearrangement models, discuss the implementation of a new representation-theoretic method of calculating evolutionary distances between circular genomes, and give the results of some initial…
Genome rearrangement has been an active area of research in computational comparative genomics for the last three decades. While initially mostly an interesting algorithmic endeavor, now the practical application by applying rearrangement…
We present a data structure called a history graph that offers a practical basis for the analysis of genome evolution. It conceptually simplifies the study of parsimonious evolutionary histories by representing both substitutions and double…
Inversions, also sometimes called reversals, are a major contributor to variation among bacterial genomes, with studies suggesting that those involving small numbers of regions are more likely than larger inversions. Deletions may arise in…
The Single Cut or Join (SCJ) operation on genomes, generalizing chromosome evolution by fusions and fissions, is the computationally simplest known model of genome rearrangement. While most genome rearrangement problems are already hard…
Genome rearrangements are events where large blocks of DNA exchange places during evolution. The analysis of these events is a promising tool for understanding evolutionary genomics, providing data for phylogenetic reconstruction based on…
The study of genome rearrangement has many flavours, but they all are somehow tied to edit distances on variations of a multi-graph called the breakpoint graph. We study a weighted 2-break distance on Eulerian 2-edge-colored multi-graphs,…
Two genomes over the same set of gene families form a canonical pair when each of them has exactly one gene from each family. Different distances of canonical genomes can be derived from a structure called breakpoint graph, which represents…
Considering a pair of genomes, the goal of rearrangement distance problems is to estimate how distant these genomes are from each other based on genome rearrangements. Seminal works in genome rearrangements assumed that both genomes being…
Genome editing allows scientists to change an organism's DNA. One promising genome editing protocol, already validated in living organisms, is based on clustered regularly interspaced short palindromic repeats (CRISPR)/Cas protein-nucleic…