Reversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information

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dc.contributor.authorAlexandrino A.O.
dc.contributor.authorOliveira A.R.
dc.contributor.authorJean G.
dc.contributor.authorFertin G.
dc.contributor.authorDias U.
dc.contributor.authorDias Z.
dc.date.accessioned2025-04-01T06:39:07Z
dc.date.available2025-04-01T06:39:07Z
dc.date.issued2023
dc.description.abstract© Mary Ann Liebert, Inc.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.e., the set of possible rearrangements allowed when we compute the distance). For the particular case of transpositions and indels on unbalanced genomes, we present a 4-approximation algorithm, improving a previous 4.5 approximation. This algorithm is extended so as to deal with gene orientation and to maintain the 4-approximation factor for the Reversal, Transposition, and Indel Distance on unbalanced genomes. Furthermore, we evaluate the proposed algorithms using experiments on simulated data.
dc.description.firstpage861
dc.description.issuenumber8
dc.description.lastpage876
dc.description.volume30
dc.identifier.doi10.1089/cmb.2023.0087
dc.identifier.issnNone
dc.identifier.urihttps://dspace.mackenzie.br/handle/10899/40463
dc.relation.ispartofJournal of Computational Biology
dc.rightsAcesso Restrito
dc.subject.otherlanguageindels
dc.subject.otherlanguageintergenic regions
dc.subject.otherlanguagereversals
dc.subject.otherlanguagetranspositions
dc.titleReversal and Transposition Distance on Unbalanced Genomes Using Intergenic Information
dc.typeArtigo de evento
local.scopus.citations0
local.scopus.eid2-s2.0-85168831079
local.scopus.subjectAlgorithms
local.scopus.subjectGene Rearrangement
local.scopus.subjectGenome
local.scopus.subjectGenomics
local.scopus.subjectINDEL Mutation
local.scopus.subjectModels, Genetic
local.scopus.updated2025-04-01
local.scopus.urlhttps://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85168831079&origin=inward
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