Difference between revisions of "FractBias"
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==Overview== | ==Overview== | ||
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| + | ==FractBias Methods== | ||
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 two genomes to compare in the [[SynMap]] tool. |
| − | ##Select the SynMap 'Syntenic Depth' option under 'Analysis Options' | + | ##Select the SynMap 'Syntenic Depth' option under 'Analysis Options.' |
| − | ##Set syntenic depth ratio | + | ##Set syntenic depth ratio between genomes (determined by empirically outside of this tool). |
#FractBias tool analysis | #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 | + | ##The syntenic genes are then parsed according to the 'target' and 'query' genomes. The genome with the lower syntenic depth ratio is set as the target genome; the genome with the higher ratio is set as the query genome. |
| + | ##A list of genes present on every target genome chromosome is made and ordered according to start site in the annotation (gff/gtf file). | ||
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| + | ##Figures are generated for every target genome chromosome (x-axis is target genome gene number in sliding window according to order of start site in genome annotation [gff]). | ||
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Revision as of 18:27, 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 Methods
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 between genomes (determined by empirically outside of this tool).
- FractBias tool analysis
- The coordinates for syntenic regions between the genomes are determined by the SynMap tool
- The syntenic genes are then parsed according to the 'target' and 'query' genomes. The genome with the lower syntenic depth ratio is set as the target genome; the genome with the higher ratio is set as the query genome.
- A list of genes present on every target genome chromosome is made and ordered according to start site in the annotation (gff/gtf file).
- Figures are generated for every target genome chromosome (x-axis is target genome gene number in sliding window according to order of start site in genome annotation [gff]).
References
</ref>http://journal.frontiersin.org/article/10.3389/fpls.2011.00002/abstract
