FractBias: a graphical tool for assessing fractionation bias following polyploidy
AffiliationBIO5 Institute, School of Plant Sciences, University of Arizona
Genetis GIDP, University of Arizona, Tucson
MetadataShow full item record
PublisherOXFORD UNIV PRESS
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/btw666
RightsCopyright © 2016, Oxford University Press.
Collection InformationThis 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 email@example.com.
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.
Note12 month embargo; Published: 22 November 2016
VersionFinal accepted manuscript
SponsorsU.S. National Science Foundation [IOS - 1339156, IOS - 1444490]