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Summary: Codon Usage Bias and Mutation Constraints Reduce the Level of Error
Minimization of the Genetic Code
Marco Archetti
DeŽ partement de Biologie, Section Ecologie et Evolution, UniversiteŽ de Fribourg, Chemin du MuseŽ e 10, 1700 Fribourg, Switzerland
Received: 25 October 2003 / Accepted: 12 February 2004 [Reviewing Editor: Martin Kreitman]
Abstract. Studies on the origin of the genetic code
compare measures of the degree of error minimiza-
tion of the standard code with measures produced by
random variant codes but do not take into account
codon usage, which was probably highly biased
during the origin of the code. Codon usage bias could
play an important role in the minimization of the
chemical distances between amino acids because the
importance of errors depends also on the frequency
of the different codons. Here I show that when codon
usage is taken into account, the degree of error
minimization of the standard code may be dramati-
cally reduced, and shifting to alternative codes often
increases the degree of error minimization. This is
especially true with a high CG content, which was
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