Distinguishing Functional Amino Acid Covariation from Background Linkage Disequilibrium in HIV Protease and Reverse Transcriptase
Figure 2
(A,A) Covariation Is Dramatically Higher Than (A,S) and (S,S) Covariation in the Specialty Dataset.
(A) Sliding window results of average D′. All mutation pairs, black; silent mutation pairs (S,S) only, green. Each sliding window contains 4% of the data points in the set. (B) Sliding window results of average D′. Amino acid mutation pairs (A,A), red; amino acid mutations to silent mutations (A,S), blue; silent mutation pairs (S,S), green. Each sliding window contains 2% of the data points in the set. (C–E) Plots of D′ against the physical distance (base) within the mutation pair for C) (A,A), D) (A,S) and E) (S,S).