Difference between revisions of "FractBias"
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FractBias is a tool used to assess fractionation bias between genomes. This is accomplished by: | FractBias is a tool used to assess fractionation bias between genomes. This is accomplished by: | ||
#User Input | #User Input | ||
| − | ## | + | ##Select two genomes to compare in the [[SynMap]] tool |
| − | ## | + | ##Select the SynMap 'Syntenic Depth' option under 'Analysis Options' |
| + | ##Set syntenic depth ratio | ||
| + | |||
| + | #FractBias tool analysis | ||
##The coordinates for syntenic regions between the genomes are determined by the SynMap tool | ##The coordinates for syntenic regions between the genomes are determined by the SynMap tool | ||
##The syntenic genes then parsed according to the 'target' and 'query' genomes are identified. The target genome is | ##The syntenic genes then parsed according to the 'target' and 'query' genomes are identified. The target genome is | ||
Revision as of 17:56, 22 September 2015
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, one may assume that fractionation would occur randomly across the redundant genes created after a WGD, however bias towards gene loss on one genome, called fractionation bias, has been observed in several species including: maize.
Overview
FractBias is a tool used to assess fractionation bias between genomes. This is accomplished by:
- User Input
- Select two genomes to compare in the SynMap tool
- Select the SynMap 'Syntenic Depth' option under 'Analysis Options'
- Set syntenic depth ratio
- FractBias tool analysis
- The coordinates for syntenic regions between the genomes are determined by the SynMap tool
- The syntenic genes then parsed according to 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.
References
</ref>http://journal.frontiersin.org/article/10.3389/fpls.2011.00002/abstract
