Istituto di Scienza e Tecnologie dell'Informazione     
Kuruoglu E. E., Arndt P. The information capacity of the genetic code: is the natural code optimal?. In: Journal of Theoretical Biology, vol. 419 pp. 227 - 237. Elsevier, 2017.
We envision the molecular evolution process as an information transfer process and provide a quantitative measure for information preservation in terms of the channel capacity according to the channel coding theorem of Shannon. We calculate Information capacities of DNA on the nucleotide (for non-coding DNA) and the amino acid (for coding DNA) level using various substitution models. We extend our results on coding DNA to a discussion about the optimality of the natural codon-amino acid code. We provide the results of an adaptive search algorithm in the code domain and demonstrate the existence of a large number of genetic codes with higher information capacity. Our results support the hypothesis of an ancient extension from a 2-nucleotide codon to the current 3-nucleotide codon code to encode the various amino acids.
URL: http://www.sciencedirect.com/science/article/pii/S0022519317300553
DOI: 10.1016/j.jtbi.2017.01.046
Subject Genetic code
Information capacity
Shannon theory
Information theory
Mutation models
Kimura model
Frozen accident
Genetic coevolution
Simulated annealing
J.3 LIFE AND MEDICAL SCIENCES. Biology and genetics
H.1.1 MODELS AND PRINCIPLES. Systems and Information Theory
G.1.6 NUMERICAL ANALYSIS. Optimization. Simulated annealing
92D10 Genetics
92D20 Protein sequences, DNA sequences
68P30 Coding and information theory
94A15 Information theory, general
94A24 Coding theorems (Shannon theory)
90C27 Combinatorial optimization
90C26 Nonconvex programming, global optimization

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