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Linearization of genome sequence graphs revisited

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dc.abstract.enThe need to include the genetic variation within a population into a reference genome led to the concept of a genome sequence graph. Nodes of such a graph are labeled with DNA sequences occurring in represented genomes. Due to double-stranded nature of DNA, each node may be oriented in one of two possible ways, resulting in marking one end of the labeling sequence as in-side and the other as out-side. Edges join pairs of sides and reflect adjacency between node sequences in genomes constituting the graph. Linearization of a sequence graph aims at orienting and ordering graph nodes in a way that makes it more efficient for visualization and further analysis, e.g. access and traversal. We propose a new linearization algorithm, called ALIBI – Algorithm for Linearization by Incremental graph BuIlding. The evaluation shows that ALIBI is computationally very efficient and generates high-quality results.
dc.affiliationUniwersytet Warszawski
dc.contributor.authorDojer, Norbert
dc.contributor.authorLisiecka, Anna
dc.date.accessioned2024-01-25T05:11:29Z
dc.date.available2024-01-25T05:11:29Z
dc.date.copyright2021-07-23
dc.date.issued2021
dc.description.accesstimeAT_PUBLICATION
dc.description.financePublikacja bezkosztowa
dc.description.number7
dc.description.versionFINAL_PUBLISHED
dc.description.volume24
dc.identifier.doi10.1016/J.ISCI.2021.102755
dc.identifier.issn2589-0042
dc.identifier.urihttps://repozytorium.uw.edu.pl//handle/item/111275
dc.identifier.weblinkhttps://api.elsevier.com/content/article/PII:S2589004221007239?httpAccept=text/xml
dc.languageeng
dc.pbn.affiliationcomputer and information sciences
dc.relation.ispartofiScience
dc.relation.pages102755:1 - 102755:14
dc.rightsCC-BY
dc.sciencecloudnosend
dc.titleLinearization of genome sequence graphs revisited
dc.typeJournalArticle
dspace.entity.typePublication