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Figure 3 | BMC Evolutionary Biology

Figure 3

From: The distribution of CTL epitopes in HIV-1 appears to be random, and similar to that of other proteomes

Figure 3

Example of the cumulative binomial probability profiles of 3 HIV-1 NEF protein sequences. Each profile features the position of predicted epitope C-terminals in the protein sequence (black dots), a running average of the C-terminal density (black line, window size 15), and the epitope-rich and/or epitope-poor regions (grey blocks) (see Eq. 1). (A + B) The distribution of CTL epitopes in the protein sequence in panel A (accession number: DQ351225) has a low probability to arise from a random distribution of CTL epitopes, based on the cumulative binomial probability method. The protein sequence in panel B (accession number: AJ233029) has a low probability to arise from a random distribution of CTL epitopes, based on the Hopkins and Skellam index of clustering, but less so according to the CBP method. (Panel A, CBP: p rich = 0.0056, p poor = 0.0062; H&S: p = 0.015. Panel B, CBP: p rich = 0.06, p poor not computable for a window size of 15 or smaller (see Methods); H&S: p < 0.001.). (C) The distribution of CTL epitopes in the protein sequence in panel C (accession number:AY905390) has a high probability to arise from a random distribution. CBP: p rich = 0.7026, p poor = 0.5328; H&S: p = 0.195. (D) The same sequence as in Panel C, but with the positions of the epitope C-terminals randomized.

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