During protein synthesis the genetic code links each codon, a triplet of nucleotides, with the corresponding amino acid. Synonymous codons are those that code for the same amino acid. The difference in the frequency of occurrence of certain synonymous codons over other synonymous codons is called the codon usage bias (CUB). The Zeng and Charlesworth model is used to estimate the strength of CUB. In their model the evolutionary process is represented by a Markov model, which allows the population size to vary over time. In this paper we propose a new method that incorporates demographic changes into the model. The method is a hybrid of two optimizers, the first is evolutionary programming and the second is a version of the genetic algorithms that uses chromosomes of variable lengths, which allows for expressing more demographic changes than what the simplified model presented by Zeng and Charlesworth does. We conduct several simulations to show why this hybridization is necessary, and also to show the superior performance of this new hybrid.
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- Evolutionary programming
- Genetic algorithm
- Non-equilibrium population
- Population genetics