We are using MATLAB's function to analyse the slidning window ka ks ratio of genes. Now, when we are considering the whole gene in question, we use the Fishers exact test for the Ka Ks ratio, however, what do we do for sliding windows ?
(http://www.mathworks.co.uk/help/bioinfo/examples/analyzing-synonymous-and-nonsynonymous-substitution-rates.html?prodcode=BI&language=en)
Hi, Good Afternoon,
Statistical tests for sliding window Ka/Ks are available in the below journal paper. Kindly go through and get the solution.
Fares, M.A., Elena, S.F., Ortiz, J., Moya, A. and Barrio, E. (2002) A sliding
window-based method to detect selective constraints in protein-coding
genes and its application to RNA viruses. J. Mol. Evol., 55, 509–521.
For your reference Kindly see the attachment pdf.
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