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FractBias: a graphical tool for assessing fractionation bias following polyploidy
Blake L Joyce1, Asher Haug-Baltzell2, Sean Davey1
1BIO5 Institute, School of Plant Sciences, University of Arizona, Tucson, AZ 85721, USA.
Summary:
Following 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.
Availability And Implementation:
FractBias is freely available as a web application at https://genomevolution.org/CoGe/SynMap.pl . The software is open source (MIT license) and executable with Python 2.7 or iPython notebook, and available on GitHub ( https://goo.gl/PaAtqy ). Documentation for FractBias is available on CoGepedia ( https://goo.gl/ou9dt6 ).
Contact:
ericlyons@email.arizona.edu.
Supplementary Information:
Supplementary data are available at Bioinformatics online.
