Approximating Rearrangement Distances with Replicas and Flexible Intergenic Regions

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dc.contributor.authorSiqueira G.
dc.contributor.authorOliveira Alexandrino A.
dc.contributor.authorRodrigues Oliveira A.
dc.contributor.authorJean G.
dc.contributor.authorFertin G.
dc.contributor.authorDias Z.
dc.date.accessioned2024-03-12T19:11:16Z
dc.date.available2024-03-12T19:11:16Z
dc.date.issued2023
dc.description.abstract© 2023, The Author(s), under exclusive license to Springer Nature Singapore Pte Ltd.Many tools from Computational Biology compute distances between genomes by counting the number of genome rearrangement events, such as reversals of a segment of genes. Most approaches to model these problems consider some simplifications such as ignoring nucleotides outside genes (the so-called intergenic regions), or assuming that just a single copy of each gene exists in the genomes. Recent works made advancements in more general models considering replicated genes and the number of nucleotides in intergenic regions. Our work aims at adapting those results by applying some flexibilization to match intergenic regions that do not have the same number of nucleotides. We propose the Signed Flexible Intergenic Reversal Distance problem, which seeks the minimum number of reversals necessary to transform one genome into the other and encodes the genomes using flexible intergenic region information while also allowing multiple copies of a gene. We show the relationship of this problem with the Signed Minimum Common Flexible Intergenic String Partition problem and use a 2k-approximation to the partition problem to show a 8k-approximation to the distance problem, where k is the maximum number of copies of a gene in the genomes.
dc.description.firstpage241
dc.description.lastpage254
dc.description.volume14248 LNBI
dc.identifier.doi10.1007/978-981-99-7074-2_19
dc.identifier.issn1611-3349
dc.identifier.urihttps://dspace.mackenzie.br/handle/10899/34165
dc.relation.ispartofLecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
dc.rightsAcesso Restrito
dc.subject.otherlanguageIntergenic Regions
dc.subject.otherlanguagePartition
dc.subject.otherlanguageRearrangement Distance
dc.subject.otherlanguageReversal
dc.titleApproximating Rearrangement Distances with Replicas and Flexible Intergenic Regions
dc.typeArtigo de evento
local.scopus.citations1
local.scopus.eid2-s2.0-85174232055
local.scopus.subjectComputational biology
local.scopus.subjectGeneral model
local.scopus.subjectGenome rearrangements
local.scopus.subjectIntergenic regions
local.scopus.subjectPartition
local.scopus.subjectPartition problem
local.scopus.subjectRearrangement distance
local.scopus.subjectRegion information
local.scopus.subjectReversal
local.scopus.subjectReversal distance
local.scopus.updated2024-12-01
local.scopus.urlhttps://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85174232055&origin=inward
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