Table 1 Related works
Author | Proteins | Drugs | Protein positions | Mutation patterns | Number of sequences | Method |
|---|---|---|---|---|---|---|
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) |