Rearrangement distance problems: An updated survey

AR Oliveira, KL Brito, AO Alexandrino… - ACM Computing …, 2024 - dl.acm.org
One of the challenges in the Comparative Genomics field is to infer how close two
organisms are based on the similarities and differences between their genetic materials …

Approximation algorithm for rearrangement distances considering repeated genes and intergenic regions

G Siqueira, AO Alexandrino, AR Oliveira… - Algorithms for Molecular …, 2021 - Springer
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 …

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

KL Brito, AR Oliveira, AO Alexandrino, U Dias… - Algorithms for Molecular …, 2021 - Springer
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 …

Reversal and indel distance with intergenic region information

AO Alexandrino, KL Brito, AR Oliveira… - … ACM transactions on …, 2022 - ieeexplore.ieee.org
Recent works on genome rearrangements have shown that incorporating intergenic region
information along with gene order in models provides better estimations for the …

Genome rearrangement distance with a flexible intergenic regions aspect

KL Brito, AO Alexandrino, AR Oliveira… - … ACM transactions on …, 2022 - ieeexplore.ieee.org
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 …

[PDF][PDF] Signed rearrangement distances considering repeated genes and intergenic regions

G Siqueira, AO Alexandrino, Z Dias - Proceedings of 14th International …, 2022 - easychair.org
Genome Rearrangement distance problems are used to infer the evolutionary distance
between genomes. These problems look at the number of mutations called rearrangement …

Signed rearrangement distances considering repeated genes, intergenic regions, and indels

G Siqueira, AO Alexandrino, Z Dias - Journal of Combinatorial Optimization, 2023 - Springer
Genome rearrangement distance problems allow to estimate the evolutionary distance
between genomes. These problems aim to compute the minimum number of mutations …

A new approach for the reversal distance with indels and moves in intergenic regions

K Lima Brito, A Rodrigues Oliveira… - RECOMB International …, 2022 - Springer
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 …

Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information

AO Alexandrino, AR Oliveira, G Jean… - Journal of …, 2023 - liebertpub.com
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 …

Transposition distance considering intergenic regions for unbalanced genomes

A Oliveira Alexandrino, A Rodrigues Oliveira… - International Symposium …, 2022 - Springer
In seminal works of genome rearrangements, the distance between two genomes is
measured by the minimum number of rearrangements (eg, reversals, transpositions, DCJs …