how to compare the Ka/Ks ratio for chromosomes
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8.7 years ago

I am interested in comparing the Ka/Ks values for each of the chromosomes in my species of interest. I have already generated Ka/Ks values for all the genes on each of the chromosome and i am now wondering how i compare the KaKs values across the chromosomes. Basically my idea is to check to see what chromosome has significant positive selection based on Ka/Ks ratios. Am i thinking correct?

Thanks
Upendra

KaKs t-test r • 3.0k views
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What organism?

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Its a plant species......Brassica rapa

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8.7 years ago

To make it more significant, you can subset on the type of genes, rather than all genes.

So, for a different subset of genes (e.g. genes involved in metabolism etc), then generate a table where each column is a subset of genes and rows are the chromosomes which would output a plot something like this

Or you can actually, plot all chromosomes on x axis (each bar is a chromosome) and bar is divided into different gene subsets, so you can compare it among all chromosomes. For significance, you can apply student t-test on that.

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