FractBias

Background

Whole genome duplications (WGDs) and genome fractionation are covered more thoroughly in other CoGepedia entries. In short, WGDs create two or more copies of a genome: which are referred to as subgenomes. The duplicate subgenomes then undergo gene loss in a process called fractionation which is part of returning to a diploid state, diploidization. All things being equal, the assumption would be that fractionation occurs in a random pattern , however bias towards gene loss on one genome, called fractionation bias, has been observed in several species including: .

Overview

FractBias is a tool used to assess fractionation bias between genomes. This is accomplished by:

1. Selecting two genomes to compare in the SynMap tool
2. The coordinates for syntenic regions between the genomes are parsed and the 'target' and 'query' genomes are identified. The target genome is

FractBias Methods

FractBias is an option that can be set within the SynMap tool.