Table 1

Positive conditional selection pressure in HIV-1 protease
Codon Y
 Codon X
 NXaYa
 NXaYs
 (Ka/Ks)Y|Xa
 NXoYa
 NXoYs
 (Ka/Ks)Y|Xo
 (Ka/Ks)Y|X
 LOD
 p
90
 73
 1879
 6
 367.63
 6842
 628
 12.79
 28.74
 >300
 <0.001
82
 24
 564
 0
 277.79
 3625
 680
 2.63
 105.8
 98.09
 <0.001
90
 95
 161
 1
 189
 7757
 595
 15.3
 12.35
 52.35
 <0.001
82
 48
 483
 2
 118.95
 3727
 663
 2.77
 42.96
 79.90
 <0.001
82
 53
 366
 2
 90.13
 4005
 694
 2.84
 31.71
 59.79
 <0.001
82
 55
 332
 2
 81.76
 3994
 701
 2.81
 29.14
 53.96
 <0.001
30
 88
 1730
 9
 71.1
 727
 677
 0.4
 179
 217.97
 <0.001
63
 50
 132
 1
 65.01
 22576
 2037
 5.46
 11.91
 21.31
 <0.001
90
 89
 329
 6
 64.37
 7677
 524
 17.2
 3.74
 100.28
 <0.001
71
 11
 126
 0
 62.06
 8775
 964
 4.48
 13.84
 21.91
 <0.001
90
 92
 315
 6
 61.63
 7706
 575
 15.73
 3.92
 95.67
 <0.001
63
 73
 1711
 14
 60.2
 20832
 2016
 5.09
 11.83
 269.97
 <0.001
33
 83
 49
 1
 57.52
 2436
 803
 3.56
 16.15
 15.09
 <0.001
90
 84
 2039
 45
 53.19
 6756
 596
 13.31
 4
 >300
 <0.001
90
 85
 395
 9
 51.52
 8361
 627
 15.65
 3.29
 117.75
 <0.001

Due to the long list of positive conditional selection pressure detected in the Specialty dataset, only the 15 positive selections with the strongest increase in (Ka/Ks)Y|Xa value after conditioning were showed here. Please see the Additional File for the complete list.

Codon X: the codon site where the first mutation appears.

Codon Y: the codon site where the second mutation appears.

(Ka/Ks)Y|Xa: conditional selection pressure of codon Y in the presence of an amino acid mutation at codon X.

(Ka/Ks)Y|Xo: conditional selection pressure of codon Y in the absence of any mutation at codon X.

LOD: confidence score for (Ka/Ks)Y|Xa > 1.

p: p-value for (Ka/Ks)Y|X > 1 to be random.

Chen and Lee Biology Direct 2006 1:14   doi:10.1186/1745-6150-1-14

Open Data