20 19-07-06

In genetics, Ka/Ks or dN/dS represents the ratio between different substitutions (Ka) and agreed substitutions (Ks). This ratio can be used to judge whether there is selection pressure on this protein coding gene.

Nucleotide mutations that do not cause amino acid changes are called synonymous mutations, and vice versa. It is generally believed that synonymous mutation is not affected by natural selection, while non-synonymous mutation is affected by natural selection. In evolutionary analysis, it is very meaningful to know the ratio of synonymous mutation and non-synonymous mutation. Commonly used parameters are synonymous mutation frequency (Ks), non-synonymous mutation frequency (Ka) and the ratio of non-synonymous mutation rate to synonymous mutation rate (Ka/Ks). If Ka/Ks & gt；; 1, which is considered to have a positive selection effect. If Ka/Ks= 1, there is a neutral choice. If ka/ks

Ks = number of synonymous mutations of SNP/number of synonymous sites.

Namely synonymous mutation rate

Ka = number of SNPs with non-synonymous mutations/number of non-synonymous sites.

That is, the non-synonymous mutation rate

Number of synonymous mutation SNP = σ synonymous SNP

Number of non-synonymous mutation SNP = σ non-synonymous SNP

Number of synonymous sites = σ synonymous sites

Number of nonsense sites = σ nonsense sites

UKa>& gtKs or Ka/Ks >>；; 1, selecting.

Uka = ks or Ka/Ks = 1+0, the gene is neutral evolution.

UKa<& ltKs or ka/ks

A function or pseudo function that detects a sequence.

Screening rapidly evolving genes (rapid evolution)

Ks can reflect the age of events.

Commonly used software in molecular evolution field

List of software for building phylogenetic tree:

Philip

Clustalw

PAML code

other

Select pressure ka/ks calculation software list:

PAML-yn00

Kaks _ calculator

K estimator

other

List of snp search software:

Polychromic

SNP detector

BGI variation analysis

The ratio (dn/ds) of non-synonymous substitution rate (amino acid change, DN) to synonymous substitution rate (amino acid unchanged, DS) is also commonly used in difference analysis. The ratio of dn/ds is 1, which indicates that the studied gene evolved under neutral selection. Less than 0. 25 represents evolution under purification selection; When the ratio is greater than 1, it is considered to have evolved under positive selection (Hurst et al., 2002; Swanson et al., 2003).

A simple and effective classification method to study the mutation of protein coding sequence is to divide substitution into synonyms.

Synonymous substitution and non-synonymous substitution. Synonymous substitution refers to those that can be cited.

It is generally believed that this substitution will not be affected by the pressure of choice or choice.

Relatively small; Non-synonymous substitutions refer to those substitutions that can change the encoded amino acids, which sometimes produce new functions.

According to the degeneracy of codons, nucleotide sites can be divided into synonymous sites and error sites.

Non-synonymous site Synonymous replacement rate and missense replacement rate are defined as: every generation or every year is the same in every possible way.

The actual number of synonymous (missense) substitutions (rS, rN) at sense (missense) sites. However, because the time of sequence differentiation is uncertain.

Therefore, synonymous substitution rate (KS or dS) and non-synonymous substitution rate (Ka or dN) can be defined as: within t years after the differentiation of two sequences, they actually occur at every possible synonymous (missense) site.

Number of synonymous (missense) substitutions. So there are: Ka = 2rNt, Ks = 2rSt. By comparing the error substitution rate and synonymous substitution rate.

The ratio can determine the selection pressure of this gene in evolution. The ratio of Kaka to Ks has been accepted and widely used.

Application index of evolutionary dynamics.

Similar to the dn/ds ratio,

The accumulation speed of nonsensical polymorphism

(pN) Scaling by Synonymous Polymorphism

(pS) provides a glimpse of the power of selectivity.

Promote the evolution of protein coding sequence.

Therefore, the ratio of genes with high pN/pS (i.e. >1).

Evolution under the influence of positive selection