How reliable re-adjustment is: correspondence regarding A. Fuglsang, "The 'effective number of codons' revisited".
A. Fuglsang [Biochem. Biophys. Res. Commun. 317 (2004) 957-964] suggested that effective number of codons for individual amino acids (Nc-values) should be re-adjusted to the number of synonymous codons of those amino acids, in order to prevent the overestimation of the effective number of codons. Here, it is shown that re-adjustment at the level of individual amino acids results in loss of considerable amounts of information. Furthermore, we have shown that theoretical Nc-values are functions of GC3s (and GC1s); as a result, when an amino acid Nc-value exceeds the related theoretical Nc-value, the implication of re-adjustment depends on the GC composition of the gene.
Marashi
Sayed-Amir
SA
Department of Biotechnology, Faculty of Science, University of Tehran, Enghelab Ave., Tehran, Iran. marashie@khayam.ut.ac.ir <marashie@khayam.ut.ac.ir>
Najafabadi
Hamed Shateri
HS
D000596:Amino Acids; D003062:Codon; D008962:Models, Theoretical
D000596:Amino Acids; D003062:Codon