Partition Based Algorithms for Rearrangement Distances with Flexible Intergenic Regions.

Genome Rearrangement distance problems are used in Computational Biology to estimate the evolutionary distance between genomes. These problems consist of minimizing the number of rearrangement events necessary to transform one genome into another. Two commonly used rearrangement events are reversal and transposition.

Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information.

The most common way to calculate the rearrangement distance between two genomes is to use the size of a minimum length sequence of rearrangements that transforms one of the two given genomes into the other, where the genomes are represented as permutations using only their gene order, based on the assumption that genomes have the same gene content. With the advance of research in genome rearrangements, new works extended the classical models by either considering genomes with different gene content (unbalanced genomes) or including more genomic characteristics to the mathematical representation of the genomes, such as the distribution of intergenic regions sizes. In this study, we study the Reversal, Transposition, and Indel (Insertion and Deletion) Distance using intergenic information, which allows comparing unbalanced genomes, because indels are included in the rearrangement model (i.

Rearrangement distance with reversals, indels, and moves in intergenic regions on signed and unsigned permutations.

Genome rearrangement events are widely used to estimate a minimum-size sequence of mutations capable of transforming a genome into another. The length of this sequence is called distance, and determining it is the main goal in genome rearrangement distance problems. Problems in the genome rearrangement field differ regarding the set of rearrangement events allowed and the genome representation.

Reversal and Indel Distance With Intergenic Region Information.

Recent works on genome rearrangements have shown that incorporating intergenic region information along with gene order in models provides better estimations for the rearrangement distance than using gene order alone. The reversal distance is one of the main problems in genome rearrangements. It has a polynomial time algorithm when only gene order is used to model genomes, assuming that repeated genes do not exist and that gene orientation is known, even when the genomes have distinct gene sets.

Genome Rearrangement Distance With a Flexible Intergenic Regions Aspect.

Most mathematical models for genome rearrangement problems have considered only gene order. In this way, the rearrangement distance considering some set of events, such as reversal and transposition events, is commonly defined as the minimum number of rearrangement events that transform the gene order from a genome G into the gene order from a genome G. Recent works initiate incorporating more information such as the sizes of the intergenic regions (i.

An improved approximation algorithm for the reversal and transposition distance considering gene order and intergenic sizes.

Background: In the comparative genomics field, one of the goals is to estimate a sequence of genetic changes capable of transforming a genome into another. Genome rearrangement events are mutations that can alter the genetic content or the arrangement of elements from the genome. Reversal and transposition are two of the most studied genome rearrangement events.

Incorporating intergenic regions into reversal and transposition distances with indels.

Problems in the genome rearrangement field are often formulated in terms of pairwise genome comparison: given two genomes [Formula: see text] and [Formula: see text], find the minimum number of genome rearrangements that may have occurred during the evolutionary process. This broad definition lacks at least two important considerations: the first being which features are extracted from genomes to create a useful mathematical model, and the second being which types of genome rearrangement events should be represented. Regarding the first consideration, seminal works in the genome rearrangement field solely used gene order to represent genomes as permutations of integer numbers, neglecting many important aspects like gene duplication, intergenic regions, and complex interactions between genes.

Labeled Cycle Graph for Transposition and Indel Distance.

In the comparative genomics field, one way to infer the evolutionary distance between two organisms of related species is by finding the minimum number of large-scale mutations, called genome rearrangements, that transform one genome into the other. This number is referred to as the . Since problems in this area emerged in the mid-1990s, several genome rearrangements have been proposed.

Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions.

The rearrangement distance is a method to compare genomes of different species. Such distance is the number of rearrangement events necessary to transform one genome into another. Two commonly studied events are the transposition, which exchanges two consecutive blocks of the genome, and the reversal, which reverts a block of the genome.

Reversals and transpositions distance with proportion restriction.

In the field of comparative genomics, one way of comparing two genomes is through the analysis of how they distinguish themselves based on a set of mutations called rearrangement events. When considering that genomes undergo different types of rearrangements, it can be assumed that some events are more common than others. To model this assumption, one can assign different weights to different events, where common events tend to cost less than others.

Genome Rearrangement Distance with Reversals, Transpositions, and Indels.

The rearrangement distance is a well-known problem in the field of comparative genomics. Given two genomes, the rearrangement distance is the minimum number of rearrangements in a set of allowed rearrangements (rearrangement model), which transforms one genome into the other. In rearrangement distance problems, a genome is modeled as a string, where each element represents a conserved region within the two genomes.

Sorting permutations by fragmentation-weighted operations.

One of the main problems in Computational Biology is to find the evolutionary distance among species. In most approaches, such distance only involves rearrangements, which are mutations that alter large pieces of the species' genome. When we represent genomes as permutations, the problem of transforming one genome into another is equivalent to the problem of Sorting Permutations by Rearrangement Operations.