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dc.contributor.authorJoyce, Blake L.
dc.contributor.authorHaug-Baltzell, Asher
dc.contributor.authorDavey, Sean
dc.contributor.authorBomhoff, Matthew
dc.contributor.authorSchnable, James C.
dc.contributor.authorLyons, Eric
dc.date.accessioned2017-05-20T00:03:53Z
dc.date.available2017-05-20T00:03:53Z
dc.date.issued2016-10-29
dc.identifier.citationBlake L. Joyce, Asher Haug-Baltzell, Sean Davey, Matthew Bomhoff, James C. Schnable, Eric Lyons; FractBias: a graphical tool for assessing fractionation bias following polyploidy. Bioinformatics 2017; 33 (4): 552-554. doi: 10.1093/bioinformatics/btw666en
dc.identifier.issn1367-4803
dc.identifier.issn1460-2059
dc.identifier.doi10.1093/bioinformatics/btw666
dc.identifier.urihttp://hdl.handle.net/10150/623554
dc.description.abstractFollowing polyploidy events, genomes undergo massive reduction in gene content through a process known as fractionation. Importantly, the fractionation process is not always random, and a bias as to which homeologous chromosome retains or loses more genes can be observed in some species. The process of characterizing whole genome fractionation requires identifying syntenic regions across genomes followed by post-processing of those syntenic datasets to identify and plot gene retention patterns. We have developed a tool, FractBias, to calculate and visualize gene retention and fractionation patterns across whole genomes. Through integration with SynMap and its parent platform CoGe, assembled genomes are pre-loaded and available for analysis, as well as letting researchers integrate their own data with security options to keep them private or make them publicly available.
dc.description.sponsorshipU.S. National Science Foundation [IOS - 1339156, IOS - 1444490]en
dc.language.isoenen
dc.publisherOXFORD UNIV PRESSen
dc.relation.urlhttps://academic.oup.com/bioinformatics/article-lookup/doi/10.1093/bioinformatics/btw666en
dc.rightsCopyright © 2016, Oxford University Pressen
dc.titleFractBias: a graphical tool for assessing fractionation bias following polyploidyen
dc.typeArticleen
dc.contributor.departmentBIO5 Institute, School of Plant Sciences, University of Arizonaen
dc.contributor.departmentGenetis GIDP, University of Arizona, Tucsonen
dc.identifier.journalBioinformaticsen
dc.description.note12 month embargo; Published: 22 November 2016en
dc.description.collectioninformationThis item from the UA Faculty Publications collection is made available by the University of Arizona with support from the University of Arizona Libraries. If you have questions, please contact us at repository@u.library.arizona.edu.en
dc.eprint.versionFinal accepted manuscripten
refterms.dateFOA2017-11-23T00:00:00Z
html.description.abstractFollowing polyploidy events, genomes undergo massive reduction in gene content through a process known as fractionation. Importantly, the fractionation process is not always random, and a bias as to which homeologous chromosome retains or loses more genes can be observed in some species. The process of characterizing whole genome fractionation requires identifying syntenic regions across genomes followed by post-processing of those syntenic datasets to identify and plot gene retention patterns. We have developed a tool, FractBias, to calculate and visualize gene retention and fractionation patterns across whole genomes. Through integration with SynMap and its parent platform CoGe, assembled genomes are pre-loaded and available for analysis, as well as letting researchers integrate their own data with security options to keep them private or make them publicly available.


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