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This paper uses the fuel cost function with valve-point effect, which increases the degree of optimization problem difficulty.
The number of tRNA genes encoded in a bacterial genome is a good measure of the degree of optimization for translational speed.
A relevant macroscopic quantity to characterize the degree of optimization of the population is the fraction ρ of structures in the population folding into the target structure.
Beneficial or compensatory mutations are systematically less probable than deleterious ones, the ratio between both types being strongly dependent on the degree of optimization of the population.
Nevertheless, the values obtained might give clues about the degree of optimization of the population and about the likeliness that fitness is improved.
For each of the codes from R, we also computed the minimization percentage, i.e., the degree of optimization that is attainable for the given code along its specific evolutionary trajectory on the fitness landscape.
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Therefore, the MST can also be a possible means to evaluate the degree of network optimization.
In general, the computational performance depends on computer architecture and the degree of code optimization.
The codon adaptation index (CAI) was used as a parameter to estimate the degree of codon optimization of a whole gene [ 56].
The observed degree of optimization seems to call for an evolutionary explanation; however there has been very little work that considers the pathways of code evolution in a realistic way.
As the optimized sequences achieve the highest absolute degree of optimization for replication rate, whereas those in the full model do not, the former does replicate faster also in the full model, when μ = 0.
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