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Table 3 Related works

From: Data-intensive analysis of HIV mutations

Author Proteins Drugs Protein positions Mutation patterns Number of sequences Method
Hoffman et al. 2003 [12] Protease PI PR10, PR12, PR13, PR14, (PR10,PR93) (PR12,PR19) 1179 Mutual
    PR15, PR19, PR20, PR30, (PR35,PR38)(PR63,PR64) (Subtype B) information
    PR32, PR35, PR36, PR37, (PR37,PR41)(PR62,PR71)   
    PR41, PR46, PR48, PR54, (PR71,PR77) (PR71,PR93)   
    PR57, PR60, PR62, PR63, (PR77,PR93)(PR12,PR19)   
    PR64, PR69, PR71, PR72, (PR15,PR77)(PR20,PR36)   
    PR73, PR77, PR82, PR84, (PR30,PR88)(PR35,PR36)   
    PR88, PR90, PR93 (PR35,PR37)(PR36,PR62)   
     (PR36,PR77)(PR46,PR82)   
     (PR46,PR84)(PR48,PR54)   
     (PR48,PR82)(PR54,PR82)   
     (PR63,PR64)(PR63,PR90)   
     (PR77,PR93)(PR84,PR90)   
     (PR73,PR90)   
Alteri et al. 2009 [13] Reverse PI, RT41, RT65, RT67, (RT215,RT41,RT210) 213 Binomial
  transcriptase NRTI, RT69, RT70, RT74, RT75, (RT60,RT103) (Subtype B) correlation
   NNRTI RT77, RT100, RT101,    coefficient,
    RT103, RT106, RT115,    Benjamini-
    RT116, RT151, RT181,    Hochberg
    RT184,RT188, RT190,    method
    RT210, RT215, RT219,    
    RT225, RT230, RT236,    
Doherty et al. 2011 [14] Protease PI PR10, PR24, PR30, (PR10,PR32,PR33, 398 Optimal
    PR32, PR33, PR43, PR46,PR47,PR54,   integer
    PR46, PR47, PR48, PR71,PR73,PR84,PR90)   programming-
    PR50, PR53, PR54, (PR10,PR33,PR43,PR46,   based
    PR71, PR73, PR74, PR54,PR71,PR82,PR84,PR90)   clustering
    PR76, PR82, PR83, (PR10,PR24,PR46,   
    PR84, PR88, PR90 PR54,PR71,PR74,PR82)   
     (PR32,PR33,PR46,PR53,   
     PR54,PR71,PR84,PR90)   
     (PR10,PR30,PR32,PR33,PR46,   
     PR54,PR71,PR84,PR88,PR90)   
     (PR10,PR33,PR43,PR46,PR48,   
     PR50,PR54,PR71,PR82)   
     (PR10,PR32,PR46,   
     PR71,PR82,PR84)   
     (PR10,PR46,PR54,PR82,PR90)   
     (PR10,PR48,PR54,PR71,   
     PR73,PR76,PR84,PR90)   
     (PR10,PR24,PR32,PR33, PR43,   
     PR46,PR54,PR71,PR82,PR84)   
     (PR10,PR24,PR30,   
     PR33,PR43,PR53,PR88)   
     (PR10,PR43,PR47,PR48,   
     PR53,PR54,PR71,PR82,PR84)   
     (PR10,PR32,PR46,   
     PR47,PR71,PR82,PR90)   
     (PR10,PR33,PR54,   
     PR73,PR84,PR90)   
     (PR10,PR46,PR71,PR84,PR90)   
     (PR10,PR54,PR71,   
     PR73,PR82,PR90)   
     (PR10,PR32,PR33,   
     PR47,PR71,PR82,PR90)   
     (PR10,PR46,PR54,   
     PR71,PR82,PR90)   
     (PR10,PR24,PR33,PR46,   
     PR54,PR71,PR82)   
     (PR10,PR48,PR54,PR82,PR90)   
     (PR10,PR32,PR43,   
     PR46,PR47,PR82)   
     (PR10,PR54,PR71,PR82)   
     (PR10,PR46,PR47,   
     PR71,PR88,PR90)   
     (PR10,PR33,PR43,PR46,   
     PR50,PR54,PR71,   
     PR73,PR82,PR90)   
     (PR10,PR33,PR46,   
     PR54,PR71,PR88,PR90)   
     (PR10,PR46,PR71,   
     PR74,PR88,PR90)   
     (PR10,PR54,PR74,PR76,PR82)   
     (PR73,PR90)   
     (PR10,PR46,PR90)   
     (PR10,PR71,PR90)   
     (PR10,PR46,PR71)   
     (PR10,PR24,PR46,PR54,PR82)   
Heider et al. 2013 [15] Reverse NRTI RT1 to RT240 (RT41,RT70, 600 Multilabel
  transcriptase    RT210,RT215) (Subtype B) classification
     (RT41,RT65,RT67,   
     RT70,RT210,RT215,RT219)   
     (RT65,RT74,RT115)   
     (RT151,RT62,RT69,   
     RT75,RT77,RT116)   
Yahi et al. 1999 [16] Protease PI, PR63, PR77,PR71, (PR10,PR46) (PR46,PR71) 287 Chi-square
  and NRTI, PR10, PR93, PR 36 (PR46,PR90) (PR71,PR82)   or Kendall
  Reverse NNRTI PR82, PR46, PR20, (PR10,PR82) (PR54,PR82)   and
  transcriptase   PR90 and PR54 (PR82,PR90) (PR71,PR90)   Fisher’s
    RT215, RT41, RT67, (PR10,PR90) (PR46,PR90)   two-tailed
    RT69, RT70, RT184, (PR54,PR90) (PR77,PR90)   
    RT210 and RT219 (PR82,PR90)   
     (RT41,RT210) (RT67,RT70)   
     (RT69,RT70) (RT70,RT219)   
     (RT41,RT210) (RT184,RT210)   
     (RT210,RT215) (RT70,RT219)   
     (RT67,RT219) (RT69,RT219)   
Melikian et al. 2013 [28] Reverse NNRTI   (RT101,RT103,RT106, 1752 Least
  transcriptase    RT181,RT188,RT190) (1681 angle
     (RT100,RT101,RT103, Subtype B) regression
     RT106,RT188,RT190)   (LARS)
     (RT101,RT181,RT190,RT227)   
     (RT100,RT101,RT181,   
     RT190,RT227)   
  1. Protease positions are represented by the prefix PR and reverse transcriptase positions by the prefix RT.