Question: Interpreting sliding windows in Ka/Ks analyses
gravatar for tlorin
5.7 years ago by
tlorin310 wrote:

Dear Biostars users,


I am running selection analysis on one gene on different species. I have performed whole sequence analyses using Ka/Ks calculator, and I was interested in finding the specific selected regions using sliding windows.

I have used the Matlab dN/dS tool for sliding windows (that is discussed Best Practices/Softwares To Calculate Ka/Ks Ratio and for which tutorial is available here). I have picked a window size of 90 and get a figure for which region between positions 25 and 40 has a Ka/Ks ratio over 1. Cool! \o/ \o/


Here is the interpretation given on the Matlab page:

"we observe several peaks over the threshold of 1. These regions appear to undergo positive selection that favors amino acid diversity, as it provides some fitness advantage."


And here is the problem: WHAT DOES IT MEAN? It surely means that there is a region under positive selection in my sequence. But WHERE?

1. Does it mean that THE WHOLE WINDOW between positions 25+90 and 40+90 is positively selected?

2. Does it mean that positive selection acts on 25-40 sites only?

3. How should I change my interpretation if I don't pick the "starting codon" visualization option, but the "middle codon" option?


You understand that picking option 1 or 2 would change completely the interpretation ;)


If anyone who has any experience with this software would like to share it it would be much appreciated!! :)

selection rna-seq matlab dn/ds • 2.6k views
ADD COMMENTlink modified 5.7 years ago by karl.schmid20 • written 5.7 years ago by tlorin310
gravatar for karl.schmid
5.7 years ago by
karl.schmid20 wrote:

Do not use sliding window analysis - they result in false positives:

Use site, branch-site models in PAML instead.

ADD COMMENTlink written 5.7 years ago by karl.schmid20
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