Related papers: Hidden breakpoints in genome alignments
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…
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.…
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…
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…
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…
A central problem in comparative genomics consists in computing a (dis-)similarity measure between two genomes, e.g. in order to construct a phylogeny. All the existing measures are defined on genomes without duplicates. However, we know…
Multiple genome alignment remains a challenging problem. Effects of recombination including rearrangement, segmental duplication, gain, and loss can create a mosaic pattern of homology even among closely related organisms. We describe a…
Genome rearrangements can be modeled as $k$-breaks, which break a genome at k positions and glue the resulting fragments in a new order. In particular, reversals, translocations, fusions, and fissions are modeled as $2$-breaks, and…
The Genome Median Problem is an important problem in phylogenetic reconstruction under rearrangement models. It can be stated as follows: given three genomes, find a fourth that minimizes the sum of the pairwise rearrangement distances…
The ability to estimate the evolutionary distance between extant genomes plays a crucial role in many phylogenomic studies. Often such estimation is based on the parsimony assumption, implying that the distance between two genomes can be…
Genome rearrangement distances are an established method in genome comparison. Works in this area may include various rearrangement operations representing large-scale mutations, gene orientation information, the number of nucleotides in…
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…
Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…
Genomic distance between two genomes, i.e., the smallest number of genome rearrangements required to transform one genome into the other, is often used as a measure of evolutionary closeness of the genomes in comparative genomics studies.…
Of the many modern approaches to calculating evolutionary distance via models of genome rearrangement, most are tied to a particular set of genomic modelling assumptions and to a restricted class of allowed rearrangements. The "position…
Many modified genetic codes are found in specific genomes in which one or more codons have been reassigned to a different amino acid from that in the canonical code. We present a model that unifies four possible mechanisms for reassignment,…
Recent advances in high-throughput genomics technologies have resulted in the sequencing of large numbers of (near) complete genomes. These genome sequences are being mined for important functional elements, such as genes. They are also…
We study complexity of rearrangement problems in the generalized breakpoint model and settle several open questions. The model was introduced by Tannier et al. (2009) who showed that the median problem is solvable in polynomial time in the…
Genome rearrangements are evolutionary events that shuffle genomic architectures. Most frequent genome rearrangements are reversals, translocations, fusions, and fissions. While there are some more complex genome rearrangements such as…
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…