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Figure 2 | Biology Direct

Figure 2

From: Evolution of the genetic code: partial optimization of a random code for robustness to translation error in a rugged fitness landscape

Figure 2

Comparison of the standard code with random alternatives for different amino acid substitution matrices and cost functions (1). Z-score is the distance, measured in standard deviations, between the mean of random code costs and the standard code cost. Ï•1, Ï•2, Ï•3 are the cost functions (1) where f(c) is the frequency of codon c; Ï•4, Ï•5, Ï•6 are the cost functions (1) for f(c) = 1 Ï•7, Ï•8, Ï•9; are the cost functions (1) where f(c) is the respective amino acid frequency; in Ï•1, Ï•4, Ï•7 p(c'|c) = 1 for any c and c' that differ by 1 nucleotide, and p(c'|c) = 0 otherwise; Ï•2, Ï•5, Ï•8 incorporate the inferred transition-transversion bias, i.e., p(c'|c) = tr b if c and c' differ by a transition, and p(c'|c) = 1 if c and c' differ by a transversion (tr b = 2 in our calculations); Ï•3, Ï•6, Ï•9 use the scheme (2).

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