The information capacity of the genetic code: Is the natural code optimal?
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.
Institute of Information Science and Technologies, "A. Faedo", CNR, via G Moruzzi 1, 56124 Pisa, Italy. Electronic address: ercan.kuruoglu@isti.cnr.it.
Ercan E
EE
Kuruoglu
Max Planck Institute for Molecular Genetics, Department of Computational Molecular Biology, Ihnestr. 63/73, 14195 Berlin, Germany.
Peter F
PF
Arndt
D000465:Algorithms; D000596:Amino Acids / Q000235:genetics; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D019143:Evolution, Molecular; D005815:Genetic Code / Q000235:genetics*; D008957:Models, Genetic
D000596:Amino Acids; D003062:Codon
DNA; Genetic code; Information capacity; Information theory; Shannon theory