Fractionation bias analysis tool for investigating whole genome duplication gene loss.
- iPythonFractBias
A version of FractBias that can be used in an interactive iPython Jupyter Notebook (http://ipython.org/notebook.html). - CommandLineFractBias
The version of FractBias that includes arguements so that a web-based platform can pass variables to complete analysis. This version is installed on the CoGe (Comparative Genomics) platform here: https://genomevolution.org/CoGe/SynMap.pl . It can be run using the SynMap tool [1].
Following polyploidy events, genomes undergo massive reduction in gene content through a process known as fractionation. Importantly, the fractionation process is not random, and there is often a bias as to which homeologous chromosome retains or loses more genes. 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, over 25,000 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.
- Docuementation for using the web-based SynMap tool can be found here: https://genomevolution.org/wiki/index.php/SynMap
- Documentation for using FractBias specifically can be found here: https://genomevolution.org/wiki/index.php/FractBias
- The SynMap Syntenic Depth option must be set for FractBias to work
- Though FractBias was originally designed to investigate genome fractionation after polyploid events, it can also be used in 1:1 comparisons to see chromosome rearrangements between species
- The example data included can be run either through iPython notebooks or the command line
- Detailed instructions for running the example data can be found in the README.md file in either the iPythonFractBias or CommandLineFractBias repo folder
- Lyons,E. et al. (2008) The value of nonmodel genomes and an example using SynMap within CoGe to dissect the hexaploidy that predates the rosids. Trop. Plant Biol., 1, 181–190
- Joyce, B.L. Haug-Baltzell, A. Davey, S., Bomhoff, M., Schnable, J.C. Lyons, E. (2016) FractBias: a graphical tool for assessing fractionation bias following polyploidy. Bioinformatics DOI: https://doi.org/10.1093/bioinformatics/btw666.
