Partition Based Algorithms for Rearrangement Distances with Flexible Intergenic Regions

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dc.contributor.authorSiqueira G.
dc.contributor.authorAlexandrino A.O.
dc.contributor.authorOliveira A.R.
dc.contributor.authorJean G.
dc.contributor.authorFertin G.
dc.contributor.authorDias Z.
dc.date.accessioned2024-11-01T06:13:35Z
dc.date.available2024-11-01T06:13:35Z
dc.date.issued2024
dc.description.abstract© 2004-2012 IEEE.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. The first studied problems ignored nucleotides outside genes (called intergenic regions), or assumed that genomes have a single copy of each gene. Recent works made advancements in more general problems considering the number of nucleotides in intergenic regions, and replicated genes. Nevertheless, genomes tend to have wildly different quantities of nucleotides on their intergenic regions, which poses a problem when comparing these regions exactly. To overcome this limitation, our work considers some flexibility when matching intergenic regions that do not have the same number of nucleotides. We propose new problems seeking the minimum number of reversals, or reversals and transpositions, necessary to transform one genome into another, while considering flexible intergenic region information. We show approximations for these problems by exploring their relationship with the Signed Minimum Common Flexible Intergenic String Partition problem. We also present different heuristics for the partition problem, and conduct experimental tests on simulated genomes to assess the performance of our algorithms.
dc.identifier.doi10.1109/TCBB.2024.3467033
dc.identifier.issnNone
dc.identifier.urihttps://dspace.mackenzie.br/handle/10899/39694
dc.relation.ispartofIEEE/ACM Transactions on Computational Biology and Bioinformatics
dc.rightsAcesso Restrito
dc.subject.otherlanguageIntergenic Regions
dc.subject.otherlanguagePartition
dc.subject.otherlanguageRearrangement Distance
dc.subject.otherlanguageReversal
dc.subject.otherlanguageTransposition
dc.titlePartition Based Algorithms for Rearrangement Distances with Flexible Intergenic Regions
dc.typeArtigo
local.scopus.citations0
local.scopus.eid2-s2.0-85205315339
local.scopus.updated2024-12-01
local.scopus.urlhttps://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85205315339&origin=inward
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