Estimating the "effective number of codons": The wright way of determining codon homozygosity leads to superior estimates

Genetics

Volumn 172, Issue 2, 2006, Pages 1301-1307

  Fuglsang, Anders ^a,b  

^a UNIVERSITY OF COPENHAGEN   (Denmark)

^b Norwegian Medicines Agency   (Norway)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; MESSENGER RNA;

ACCURACY; ARTICLE; CODON; CODON USAGE; CORRELATION ANALYSIS; ESCHERICHIA COLI; GENE; GENE NUMBER; GENE STRUCTURE; GENETIC ANALYSIS; GENETIC CODE; HOMOZYGOSITY; MATHEMATICAL GENETICS; MATHEMATICAL MODEL; NUCLEOTIDE SEQUENCE; POPULATION GENETICS; PRIORITY JOURNAL; RNA ANALYSIS; SAMPLING;

CODON; COMPUTER SIMULATION; ESCHERICHIA COLI; HOMOZYGOTE; MODELS, GENETIC; RNA, MESSENGER; STATISTICS, NONPARAMETRIC;

ESCHERICHIA COLI;

EID: 33644784817     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.105.049643     Document Type: Article

References (13)

1. BANERJEE, T., S. K. GUPTA and T. C. GHOSH, 2005 Towards a resolution on the inherent methodological weakness of the "effective number of codons used by a gene." Biochem. Biophys. Res. Commun. 330: 1015-1018.
2. BERNSTEIN, J. A., A. B. KHODURSKY, P. H. LIN, S. LIN-CHAO and S. N. COHEN, 2002 Global analysis of mRNA decay and abundance in Escherichia coli at single-gene resolution using two-color fluorescent DNA microarrays. Proc. Natl. Acad. Sci. USA 99: 9697-9702.
3. COMERON, J. M., and M. AGUADE, 1998 An evaluation of measures of synonymous codon usage bias. J. Mol. Evol. 47: 268-274.
4. EYRE-WALKER, A., 1996 Synonymous codon usage bias is related to gene length in Escherichia coli: Selection for translational accuracy? Mol. Biol. Evol. 13: 864-872.
5. FUGLSANG, A., 2004 The 'effective number of codons' revisited. Biochem. Biophys. Res. Commun. 317: 957-964.
6. FUGLSANG, A., 2005 On the methodological weakness of 'the effective number of codons': a reply to Marashi and Najafabadi. Biochem. Biophys. Res. Commun. 327: 1-3.
7. GOETZ, R. M., and A. FUGLSANG, 2005 Correlation of codon bias measures with mRNA levels: analysis of transcriptome data from Escherichia coli. Biochem. Biophys. Res. Commun. 327: 4-7.
8. GOUY, M., and C. GAUTIER, 1982 Codon usage in bacteria: correlation with gene expressivity. Nucleic Acids Res. 10: 7055-7074.
9. IKEMURA, T., 1981 Correlation between the abundance of Escherichia coli transfer RNAs and the occurrence of the respective codons in its protein genes. J. Mol. Biol. 146: 1-21.
10. IKEMURA, T., 1985 Codon usage and tRNA content in unicellular and multicellular organisms. Mol. Biol. Evol. 2: 13-34.
11. MARASHI, S.-A., AND H. S. NAJAFABADI, 2004 How reliable re-adjustment is: correspondence regarding A. Fuglsang, "the effective number of codons revisited." Biochem. Biophys. Res. Commun. 324: 1-2.
12. SHARP, P. M., and W.-H. LI, 1987 The codon adaptation index - a measure of directional synonymous codon usage bias, and its potential applications. Nucleic Acids Res. 15: 1281-1295.
13. WRIGHT, F., 1990 The 'effective number of codons' used in a gene. Gene 87: 23-29.