|
Liu et al. 2008 [7]
|
Protease
|
PI
|
PR1 to PR99
|
(PR30 PR75 PR88),
|
7758+8761 (Subtype B and non-Subtype B)
|
k-way clustering
|
| | | | |
(PR1–PR9 PR12–PR15
| | |
| | | | |
PR17 PR19 PR20 PR22
| | |
| | | | |
PR25 PR26 PR28
| | |
| | | | |
PR31 PR35–PR42
| | |
| | | | |
PR45 PR49 PR52)
| | |
| | | | |
(PR56 PR57 PR59
| | |
| | | | |
PR61 PR65 PR68–PR70
| | |
| | | | |
PR77 PR83 PR87
| | |
| | | | |
PR89 PR96–PR99)
| | |
| | | | |
(PR1 PR2 PR9 PR26 PR30
| | |
| | | | |
PR40 PR45 PR56
| | |
| | | | |
PR59 PR75 PR81 PR88 PR98)
| | |
| | | | |
(PR13–PR15 PR20 PR35–PR38
| | |
| | | | |
PR41 PR42 PR49 PR57
| | |
| | | | |
PR69 PR70 PR77 PR83 PR89)
| | |
| | | | |
(PR10 PR23 PR24
| | |
| | | | |
PR27 PR32–PR34 PR43
| | |
| | | | |
PR46–PR48 PR50 PR53–PR55
| | |
| | | | |
PR58 PR71 PR76 PR80 PR82)
| | |
| | | | |
(PR30 PR75 PR88)
| | |
| | | | |
(PR1 PR2 PR9 PR26
| | |
| | | | |
PR40 PR45 PR59 PR87 PR98)
| | |
| | | | |
(PR13–PR15 PR20 PR35–PR38
| | |
| | | | |
PR41 PR49 PR57 PR69
| | |
| | | | |
PR70 PR77 PR83 PR89)
| | |
| | | | |
(PR10 PR23 PR24
| | |
| | | | |
PR27 PR32–PR34
| | |
| | | | |
PR42 PR43 PR46–PR48
| | |
| | | | |
PR50 PR53–PR55
| | |
| | | | |
PR58 PR71PR76 PR80 PR82)
| | |
|
Reuman et al. 2010 [8]
|
Reverse transcriptase
|
NNRTI
|
RT90, RT94, RT98,
|
(RT101,RT181,RT190)
|
13039
|
Jaccard similarity
|
| | | |
RT100, RT101, RT102
|
(RT103,RT181,RT190)
|
(10504 Subtype B,
|
coefficient,
|
| | | |
RT103, RT105, RT106,
|
(RT108,RT181,RT221)
|
747 Subtype C,
|
Holm’s correction,
|
| | | |
RT108, RT138,
|
(RT98,RT181,RT190)
|
363 (CRF) 01_AE,
|
Poissoness plot
|
| | | |
RT139, RT178, RT179,
|
(RT181,RT190,RT221)
|
210 Subtype A,
| |
| | | |
RT181, RT188,
|
(RT103,RT181,RT221)
|
320 CRF 02_AG,
| |
| | | |
RT190, RT221, RT223,
|
(RT103,RT108,RT221)
|
895 others)
| |
| | | |
RT225, RT227,
|
(RT101,RT108,RT181)
| | |
| | | |
RT230, RT232,
|
(RT101,RT108,RT190)
| | |
| | | |
RT234, RT236,
|
(RT103,RT108,RT181)
| | |
| | | |
RT237, RT238,
|
(RT108,RT190,RT221)
| | |
| | | |
RT241, RT242, RT318
|
(RT98,RT108,RT181)
| | |
| | | | |
(RT98,RT101,RT190)
| | |
| | | | |
(RT98,RT101,RT181)
| | |
| | | | |
(RT101,RT181,RT190)
| | |
| | | | |
(RT101,RT181,RT221)
| | |
| | | | |
(RT98,RT103,RT108)
| | |
| | | | |
(RT101,RT181,RT190)
| | |
| | | | |
(RT108,RT181,RT190)
| | |
| | | | |
(RT98,RT103,RT181)
| | |
|
Wu et al. 2003 [10]
|
Protease
|
PI
|
PR1 to PR99
|
(PR10 PR63
|
2244 (Subtype B)
|
binomial correlation
|
| | | | |
PR71 PR73 PR90)
| |
coefficients, pca
|
| | | | |
(PR10 PR63
| | |
| | | | |
PR71 PR90 PR93)
| | |
| | | | |
(PR10 PR62
| | |
| | | | |
PR63 PR90 PR93)
| | |
| | | | |
(PR10 PR62
| | |
| | | | |
PR63 PR73 PR90)
| | |
| | | | |
(PR10 PR20
| | |
| | | | |
PR71 PR73 PR90)
| | |
| | | | |
(PR10 PR20
| | |
| | | | |
PR62 PR73 PR90)
| | |
| | | | |
(PR10 PR46
| | |
| | | | |
PR71 PR90 PR93)
| | |
| | | | |
(PR10 (PR30)
| | |
| | | | |
PR73 PR84 PR90)
| | |
| | | | |
(PR10 (PR30)
| | |
| | | | |
PR46 PR84 PR90)
| | |
| | | | |
(PR10 PR71 PR73 PR84 PR90)
| | |
| | | | |
(PR10 PR46 PR71 PR84 PR90)
| | |
| | | | |
(PR10 PR24 PR46
| | |
| | | | |
PR10 PR46 PR90)
| | |
| | | | |
(PR10 (PR30)
| | |
| | | | |
PR46 PR54 PR82)
| | |
| | | | |
(PR10 PR48 PR54 PR82)
| | |
| | | | |
(PR10 PR24
| | |
| | | | |
PR46 PR54 PR82)
| | |
| | | | |
(PR32 PR46 PR82)
| | |
| | | | |
(PR10 PR46 PR53
| | |
| | | | |
PR54 PR71 PR82)
| | |
| | | | |
(PR30 (PR82) PR88)
| | |
| | | | |
(PR13 PR30 PR88)
| | |
| | | | |
(PR30 PR75 PR88)
| | |
| | | | |
(PR10 PR46
| | |
| | | | |
PR63 PR71 PR93)
| | |
| | | | |
(PR20 PR36 PR54)
| | |
| | | | |
(PR10 PR20 PR54 PR71)
| | |
| | | | |
(PR63 (PR64) PR71)
| | |
| | | | |
(PR10 PR77 PR93)
| | |
| | | | |
(PR20 PR36 PR62)
| | |
| | | | |
(PR20 PR35 PR36 (PR77))
| | |
| | | | |
(PR15 PR20 PR36 (PR77))
| | |
| | | | |
(PR10 PR24 PR89)
| | |
| | | | |
(PR10 PR20 PR73)
| | |
| | | | |
(PR10 PR73 PR77)
| | |
