Normally dN/dS ratios are calculated and interpreted as below one negative selection, above 1 is positive selection and 1 means neutral selection. How to interpret dS/dN ratios? Programs like SNAP provides dS/dN graphs and ratios.
For example:
Averages of all pairwise comparisons: ds = 0.1678, dn = 0.4090, ds/dn = 0.4072, ps/pn = 0.4707
Please see image as well.
Can somebody explains it in simple words as I am not much familiar with this?
dN/dS measured across the whole protein sequence between two divergent species in theory tells you something about selection. If this ratio = 1, then the whole coding sequence evolves neutrally, when 0 < dN/dS < 1, it's under constraint, and when > 1 under positive selection. However in real data, you will never see this ratio going close to 1, because most amino acid positions on the sequence are functionally constraint. In other words, almost all coding sequences on average should have 0 < dN/dS < 1. This ratio is usually between 0.2 to 0.3 on average for typical proteins. Nevertheless, there could be sites under positive selection, whose signal may be "masked" by averaging across the whole sequence. This is why people developed "site-models" to allow for rate heterogeneity of dN/dS across different amino acid positions (see CodeML).
Dear Artur,
Thanks for your reply. My question is simple. If dS/dN is 1, less than 1 and above1, what does it indicate in terms of positive selection, negative selection and neutral selection?
Regards,
Shahid
Dear Artur,
Attached paper describes these terms at page 5 for dN/dS ratios.
Evolutionary analysis
A pairwise comparison bioinformatics approach (SNAP)
was applied to determine the synonymous and non-synonymous
substitution rates and selective evolutionary
pressure for the F protein. The results are presented in the
Fig. 3, in which numbers above one indicate the positive
selection, around one show the neutral selection, whereas
below one indicate the negative or purifying selection.
dN/dS measured across the whole protein sequence between two divergent species in theory tells you something about selection. If this ratio = 1, then the whole coding sequence evolves neutrally, when 0 < dN/dS < 1, it's under constraint, and when > 1 under positive selection. However in real data, you will never see this ratio going close to 1, because most amino acid positions on the sequence are functionally constraint. In other words, almost all coding sequences on average should have 0 < dN/dS < 1. This ratio is usually between 0.2 to 0.3 on average for typical proteins. Nevertheless, there could be sites under positive selection, whose signal may be "masked" by averaging across the whole sequence. This is why people developed "site-models" to allow for rate heterogeneity of dN/dS across different amino acid positions (see CodeML).
Rongfeng Cui question was not about dn/ds, but it was regarding ds/dn ratio?
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