Sorting signed permutations by intergenic reversals

AR Oliveira, G Jean, G Fertin, KL Brito… - … ACM transactions on …, 2020 - ieeexplore.ieee.org
Genome rearrangements are mutations affecting large portions of a genome, and a reversal
is one of the most studied genome rearrangements in the literature through the Sorting by …

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 …

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 …

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 …

Reversal and transposition distance of genomes considering flexible intergenic regions

KL Brito, AR Oliveira, AO Alexandrino, U Dias… - Procedia Computer …, 2021 - Elsevier
Biologists have proposed a vast list of problems heavily studied by mathematicians,
computer scientists, and statisticians. From a theoretical point of view, biology can inspire …

A new 1.375-approximation algorithm for sorting by transpositions

LAG Silva, LAB Kowada, NR Rocco… - Algorithms for Molecular …, 2022 - Springer
Background sorting by transpositions (SBT) is a classical problem in genome
rearrangements. In 2012, SBT was proven to be NP-hard and the best approximation …

Genome Rearrangement Analysis: Cut and Join Genome Rearrangements and Gene Cluster Preserving Approaches

THM Middendorf, M Bernt - Comparative Genomics - Springer
Genome rearrangements are mutations that change the gene content of a genome or the
arrangement of the genes on a genome. Several years of research on genome …

Reversals Distance Considering Flexible Intergenic Regions Sizes

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

Varia\c {c}\~ oes do Problema de Dist\^ ancia de Rearranjos

AO Alexandrino - arxiv preprint arxiv:2404.17996, 2024 - arxiv.org
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 …

Um novo algoritmo 1.375-aproximativo baseado em grupos de permutações para o Problema da Ordenação por Transposições

LAG Silva - 2022 - realp.unb.br
O Problema da Ordenação por Transposições (SBT, sigla dos termos em língua inglesa
Sorting By Transpositions) é um problema clássico em rearranjos de genoma. Em 2012 …