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Table 2 Related works

From: Data-intensive analysis of HIV mutations

Author Proteins Drugs Protein positions Mutation patterns Number of sequences Method
Rhee et al. 2004 [9] Protease PI, PR24, PR30, PR32, (PR30,PR88) (PR46,PR90) 2795  
  and Reverse NRTI, PR46, PR47, PR48, (PR73,PR90) (27 Subtype C,  
  transcriptase NNRTI PR50, PR53, PR54, (PR54,PR82,PR90) 15 Subtype A,  
    PR73, PR82, PR84, (PR24,PR46,PR54,PR82) 7 Subtype D,  
    PR88, PR90 (PR73,PR84,PR90) 2746 Subtype B)  
    RT41, RT44, RT62, (PR46,PR54,PR82,PR90)   
    RT65, RT67, RT69, (PR84,PR90) (PR46,PR88)   
    RT70, RT74, RT115, (PR46,PR73,PR90) (PR54,PR82)   
    RT116, RT118, RT151, (PR46,PR84,PR90)   
    RT184, RT210, (PR46,PR54,PR82,PR90)   
    RT215, RT219 (PR46,PR73,PR84 PR90)   
     (PR30,PR88,PR90)   
     (PR48,PR54,PR82),   
     (PR32,PR46,PR82,PR90)   
     (PR24,PR46,PR54,PR82)   
     (PR53,PR54,PR82,PR90)   
     (PR24,PR46,PR82) (PR46,PR82)   
     (PR46,PR90) (PR30,PR46,PR88)   
     (RT41, RT184, RT215)   
     (RT41, RT184, RT210)   
     (RT41, RT215)   
     (RT67, RT70, RT184, RT219)   
     (RT70, RT184)   
     (RT41, RT210, RT215)   
     (RT184, RT215)   
     (RT41, RT118, RT184)   
     (RT210, RT215)   
     (RT41, RT67, RT118, RT210, RT215)   
     (RT74, RT184)   
     (RT67, RT70, RT184)   
     (RT67, RT69, RT70, RT184, RT219)   
     (RT41, RT67, RT184,   
     RT210, RT215)   
     (RT41, RT184)   
     (RT62, RT184)   
     (RT41, RT44, RT67, RT118)   
     (RT184, RT210, RT215)   
     (RT67, RT70, RT184, RT215, RT219)   
     (RT67, RT70, RT219)   
     (RT67, RT70)   
     (RT41, RT184, RT215)   
     (RT41, RT118, RT210, RT215)   
     (RT41, RT67, RT210, RT215)   
     (RT69, RT70)   
     (RT41, RT44, RT67, RT118,   
     RT210, RT215)   
     (RT41, RT74, RT184, RT215, RT69)   
     (RT103 RT181)   
     (RT100 RT103)(RT103 RT108)   
     (RT101 RT190)   
     (RT103 RT225)   
     (RT103 RT181 RT190)   
     (RT103 RT190)   
     (RT181 RT190)   
     (RT103 RT238)(RT101 RT103)   
     (RT108 RT181)   
     (RT101 RT181 RT190)   
     (RT98 RT103)   
     (RT103 RT108 RT181)   
     (RT103 RT188)(RT103 RT230)   
Gonzales et al. 2003 [11] Protease PI, RT41, RT62, RT65, (RT41,RT184,RT215) 487 Fisher’s
  and Reverse NRTI, RT67, RT69, RT70, (RT41,RT184,RT210,RT215) (Subtype B) exact
  transcriptase NNRTI RT74, RT75, RT77, (RT67,RT70,RT215,RT219)   test,
    RT115, RT116, RT151, (RT41,RT67,RT69,RT210,RT215)   Benjamini-
    RT184, RT210, (RT41,RT67,RT184,RT210,   Hochberg,
    RT215, and RT219 RT215,RT219)   K-medoids
    PR24, PR30, PR32, (RT41,RT67,RT69,RT70,   
    PR46, PR47, PR48, RT184,RT215,RT219)   
    PR50, PR53, PR54, (RT65,RT70,RT75,RT77,RT115„   
    PR73, PR88, PR82, RT116,RT151,RT184,RT219)   
    PR84, and PR90 (PR54,PR73,PR84,PR90)   
     (PR46,PR84,PR90)   
     (PR24,PR46,PR54,PR82)   
     (PR46,PR54,PR82,PR90)   
     (PR48,PR,54,PR82)   
Sing et al. 2005 [6] Reverse NRTI RT41, RT43, RT44, RT62, (RT41, RT210,RT215) 1355 hierarchical
  transcriptase   RT67, RT69, RT70, (RT67,RT70,RT219)   clustering,
    RT74, RT75, RT77,    Fisher’s
    RT116, RT118, RT151,    exact test
    RT203, RT208,    
    RT210, RT215, RT215,    
    RT218, RT219,    
    RT219, RT223,    
    RT228, RT228    
Brehm et al. 2012 [41] Reverse NNRTI   (RT184,RT348) 12  
  transcriptase     (Subtype C)  
  1. Protease positions are represented by the prefix PR and reverse transcriptase positions by the prefix RT.