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dc.contributor.author
Glover, Natasha M.
dc.contributor.author
Altenhoff, Adrian
dc.contributor.author
Dessimoz, Christophe
dc.date.accessioned
2019-06-19T15:28:08Z
dc.date.available
2019-01-26T15:33:26Z
dc.date.available
2019-04-01T15:09:44Z
dc.date.available
2019-06-19T15:28:08Z
dc.date.issued
2019-01-11
dc.identifier.issn
2167-8359
dc.identifier.other
10.7717/peerj.6231
en_US
dc.identifier.uri
http://hdl.handle.net/20.500.11850/320057
dc.identifier.doi
10.3929/ethz-b-000320057
dc.description.abstract
n polyploid genomes, homoeologs are a specific subtype of homologs, and can be thought of as orthologs between subgenomes. In Orthologous MAtrix, we infer homoeologs in three polyploid plant species: upland cotton (Gossypium hirsutum), rapeseed (Brassica napus), and bread wheat (Triticum aestivum). While we can typically recognize the features of a “good” homoeolog prediction (a consistent evolutionary distance, high synteny, and a one-to-one relationship), none of them is a hard-fast criterion. We devised a novel fuzzy logic-based method to assign confidence scores to each pair of predicted homoeologs. We inferred homoeolog pairs and used the new and improved method to assign confidence scores, which ranged from 0 to 100. Most confidence scores were between 70 and 100, but the distribution varied between genomes. The new confidence scores show an improvement over our previous method and were manually evaluated using a subset from various confidence ranges.
en_US
dc.format
application/pdf
en_US
dc.language.iso
en
en_US
dc.publisher
PeerJ
en_US
dc.rights.uri
http://creativecommons.org/licenses/by/4.0/
dc.subject
Homoeology
en_US
dc.subject
Fuzzy logic
en_US
dc.subject
Polyploidy
en_US
dc.subject
Confidence scores
en_US
dc.subject
Comparative genomics
en_US
dc.title
Assigning confidence scores to homoeologs using fuzzy logic
en_US
dc.type
Journal Article
dc.rights.license
Creative Commons Attribution 4.0 International
ethz.journal.title
PeerJ
ethz.journal.volume
6
en_US
ethz.journal.abbreviated
PeerJ
ethz.pages.start
e6231
en_US
ethz.size
19 p.
en_US
ethz.version.deposit
publishedVersion
en_US
ethz.identifier.wos
ethz.identifier.pubmed
30648004
ethz.publication.place
London
en_US
ethz.publication.status
published
en_US
ethz.date.deposited
2019-01-26T15:33:27Z
ethz.source
WOS
ethz.eth
yes
en_US
ethz.availability
Open access
en_US
ethz.rosetta.installDate
2019-06-19T15:28:23Z
ethz.rosetta.lastUpdated
2019-06-19T15:28:23Z
ethz.rosetta.versionExported
true
ethz.COinS
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