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Table 3 Log-likelihood Values and Parameter Estimates of the different physicochemical properties for the MHC data.

From: Identification of physicochemical selective pressure on protein encoding nucleotide sequences

Data set/Model

loglikelihood

κ

ω

γ

proportions

MHC Class I

     

Volume

     

Model A1

-2463.35

2.86

0.22, 8.74

0.00, 3.47

Prob (ω0, γ0) = 0.73

     

Prob (ω0, γ1) = 0.17

     

Prob (ω1, γ0) = 0.07

     

Prob (ω1, γ1) = 0.03

Model A2

-2474.61

2.84

0.23, 9.30

0.53

Prob (ω0, γ0) = 0.90

     

Prob (ω1, γ0) = 0.10

Hydrophobicity

     

Model A1

-2464.89

2.81

0.14, 9.94

0.12, 5.48

Prob (ω0, γ0) = 0.80

     

Prob (ω0, γ1) = 0.09

     

Prob (ω1, γ0) = 0.07

     

Prob (ω1, γ1) = 0.04

Model A2

-2505.65

2.59

0.09, 9.12

0.62

Prob (ω0, γ0) = 0.87

     

Prob (ω1, γ0) = 0.13

Charge

     

Model A1

-2470.99

2.75

0.00, 5.46

0.19, 5.48

Prob (ω0, γ0) = 0.76

     

Prob (ω0, γ1) = 0.05

     

Prob (ω1, γ0)) = 0.11

     

Prob (ω1, γ1) = 0.08

Model A2

-2515.343693

2.59

0.37,18.77

0.65

Prob (ω0, γ0) = 0.94

     

Prob (ω1, γ0) = 0.06

Polarity

     

Model A1

-2470.149113

2.93

0.17, 6.99

0.02, 3.85

Prob (ω0, γ0) = 0.75

     

Prob (ω0, γ1) = 0.12

     

Prob (ω1, γ0) = 0.04

     

Prob (ω1, γ1) = 0.08

Model A2

-2491.533373

2.89

0.18,7.75

0.61

Prob (ω0, γ0) = 0.88

     

Prob (ω1, γ0) = 0.12