Assignment of orthologous genes in unbalanced genomes using cycle packing of adjacency graphs

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dc.contributor.authorSiqueira G.
dc.contributor.authorOliveira A.R.
dc.contributor.authorAlexandrino A.O.
dc.contributor.authorJean G.
dc.contributor.authorFertin G.
dc.contributor.authorDias Z.
dc.date.accessioned2024-07-01T06:11:49Z
dc.date.available2024-07-01T06:11:49Z
dc.date.issued2024
dc.description.abstract© The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2024.The adjacency graph is a structure used to model genomes in several rearrangement distance problems. In particular, most studies use properties of a maximum cycle packing of this graph to develop bounds and algorithms for rearrangement distance problems, such as the reversal distance, the reversal and transposition distance, and the double cut and join distance. When each genome has no repeated genes, there exists only one cycle packing for the graph. However, when each genome may have repeated genes, the problem of finding a maximum cycle packing for the adjacency graph (adjacency graph packing) is NP-hard. In this work, we develop a randomized greedy heuristic and a genetic algorithm heuristic for the adjacency graph packing problem for genomes with repeated genes and unequal gene content. We also propose new algorithms with simple implementation and good practical performance for reversal distance and reversal and transposition distance in genomes without repeated genes, which we combine with the heuristics to find solutions for the problems with repeated genes. We present experimental results and compare the application of these heuristics with the application of the MSOAR framework in rearrangement distance problems. Lastly, we apply our genetic algorithm heuristic to real genomic data to validate its practical use.
dc.identifier.doi10.1007/s10732-024-09528-z
dc.identifier.issnNone
dc.identifier.urihttps://dspace.mackenzie.br/handle/10899/38815
dc.relation.ispartofJournal of Heuristics
dc.rightsAcesso Restrito
dc.subject.otherlanguageCycle packing
dc.subject.otherlanguageGenome rearrangements
dc.subject.otherlanguageIndels
dc.subject.otherlanguageReversals
dc.subject.otherlanguageTransposition
dc.titleAssignment of orthologous genes in unbalanced genomes using cycle packing of adjacency graphs
dc.typeArtigo
local.scopus.citations1
local.scopus.eid2-s2.0-85194743402
local.scopus.subjectAdjacency graphs
local.scopus.subjectCycle packing
local.scopus.subjectGenome rearrangements
local.scopus.subjectGraph packing
local.scopus.subjectIndel
local.scopus.subjectMaximum cycle packings
local.scopus.subjectReversal
local.scopus.subjectReversal distance
local.scopus.subjectTransposition
local.scopus.subjectTransposition distances
local.scopus.updated2025-04-01
local.scopus.urlhttps://www.scopus.com/inward/record.uri?partnerID=HzOxMe3b&scp=85194743402&origin=inward
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