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https://hdl.handle.net/1959.11/43760
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DC Field | Value | Language |
---|---|---|
dc.contributor.author | Brankovic, Ljiljana | en |
dc.contributor.author | Iliopoulos, Costas S | en |
dc.contributor.author | Kundu, Ritu | en |
dc.contributor.author | Mohamad, Manal | en |
dc.contributor.author | Pissis, Solon P | en |
dc.contributor.author | Vayani, Fatima | en |
dc.date.accessioned | 2022-02-23T02:50:17Z | - |
dc.date.available | 2022-02-23T02:50:17Z | - |
dc.date.issued | 2016-01-04 | - |
dc.identifier.citation | Theoretical Computer Science, 609(2), p. 374-383 | en |
dc.identifier.issn | 1879-2294 | en |
dc.identifier.issn | 0304-3975 | en |
dc.identifier.uri | https://hdl.handle.net/1959.11/43760 | - |
dc.description.abstract | DNA sequencing is the process of determining the exact order of the nucleotide bases of an individual's genome in order to catalogue sequence variation and understand its biological implications. Whole-genome sequencing techniques produce masses of data in the form of short sequences known as reads. Assembling these reads into a whole genome constitutes a major algorithmic challenge. Most assembly algorithms utilise de Bruijn graphs constructed from reads for this purpose. A critical step of these algorithms is to detect typical motif structures in the graph caused by sequencing errors and genome repeats, and filter them out; one such complex subgraph class is a so-called <i>superbubble</i>. In this paper, we propose an O(<i>n</i> + <i>m</i>)-time algorithm to detect all superbubbles in a directed acyclic graph with <i>n</i> vertices and <i>m</i> (directed) edges, improving the best-known O(<i>m</i> log <i>m</i>)-time algorithm by Sung et al. | en |
dc.language | en | en |
dc.publisher | Elsevier BV | en |
dc.relation.ispartof | Theoretical Computer Science | en |
dc.rights | Attribution 4.0 International | * |
dc.rights.uri | http://creativecommons.org/licenses/by/4.0/ | * |
dc.title | Linear-time superbubble identification algorithm for genome assembly | en |
dc.type | Journal Article | en |
dc.identifier.doi | 10.1016/j.tcs.2015.10.021 | en |
dcterms.accessRights | UNE Green | en |
local.contributor.firstname | Ljiljana | en |
local.contributor.firstname | Costas S | en |
local.contributor.firstname | Ritu | en |
local.contributor.firstname | Manal | en |
local.contributor.firstname | Solon P | en |
local.contributor.firstname | Fatima | en |
local.profile.school | School of Science and Technology | en |
local.profile.email | lbrankov@une.edu.au | en |
local.output.category | C1 | en |
local.record.place | au | en |
local.record.institution | University of New England | en |
local.publisher.place | Netherlands | en |
local.format.startpage | 374 | en |
local.format.endpage | 383 | en |
local.peerreviewed | Yes | en |
local.identifier.volume | 609 | en |
local.identifier.issue | 2 | en |
local.access.fulltext | Yes | en |
local.contributor.lastname | Brankovic | en |
local.contributor.lastname | Iliopoulos | en |
local.contributor.lastname | Kundu | en |
local.contributor.lastname | Mohamad | en |
local.contributor.lastname | Pissis | en |
local.contributor.lastname | Vayani | en |
dc.identifier.staff | une-id:lbrankov | en |
local.profile.orcid | 0000-0002-5056-4627 | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.profile.role | author | en |
local.identifier.unepublicationid | une:1959.11/43760 | en |
local.date.onlineversion | 2015-10-23 | - |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
dc.identifier.academiclevel | Academic | en |
local.title.maintitle | Linear-time superbubble identification algorithm for genome assembly | en |
local.output.categorydescription | C1 Refereed Article in a Scholarly Journal | en |
local.search.author | Brankovic, Ljiljana | en |
local.search.author | Iliopoulos, Costas S | en |
local.search.author | Kundu, Ritu | en |
local.search.author | Mohamad, Manal | en |
local.search.author | Pissis, Solon P | en |
local.search.author | Vayani, Fatima | en |
local.open.fileurl | https://rune.une.edu.au/web/retrieve/d5dfc2fd-028a-43f2-be84-d6a541211d23 | en |
local.uneassociation | No | en |
local.atsiresearch | No | en |
local.sensitive.cultural | No | en |
local.year.available | 2015 | en |
local.year.published | 2016 | en |
local.fileurl.open | https://rune.une.edu.au/web/retrieve/d5dfc2fd-028a-43f2-be84-d6a541211d23 | en |
local.fileurl.openpublished | https://rune.une.edu.au/web/retrieve/d5dfc2fd-028a-43f2-be84-d6a541211d23 | en |
local.subject.for2020 | 461305 Data structures and algorithms | en |
local.subject.for2020 | 460199 Applied computing not elsewhere classified | en |
local.subject.seo2020 | 229999 Other information and communication services not elsewhere classified | en |
Appears in Collections: | Journal Article School of Science and Technology |
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File | Description | Size | Format | |
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openpublished/LinearTimeBrankovic2016JournalArticle.pdf | Published version | 351.9 kB | Adobe PDF Download Adobe | View/Open |
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