Effective number of codons explained

Effective number of codons (abbreviated as ENC or Nc) is a measure to study the state of codon usage biases in genes and genomes.^[1] The way that ENC is computed has obvious similarities to the computation of effective population size in population genetics.^[2] Although it is easy to compute ENC values, it has been shown that this measure is one of the best measures to show codon usage bias.^[3]

Since the original suggestion of the ENC, several investigators have tried to improve the method,^{[4] [5]} but it seems that there is much room to improve this measure.^{[6] [7] [8] [9] [10] [11]}

Notes and References

1. Wright F. . The 'effective number of codons' used in a gene. . Gene . 87 . 1 . 23–29 . 1990 . 2110097 . 10.1016/0378-1119(90)90491-9.
2. Kimura, M. . Crow, J.F. . amp . The number of alleles that can be maintained in a finite population.. Genetics . 49 . 725–738 . 1964 . 4 . 10.1093/genetics/49.4.725 . 14156929 . 1210609.
3. Comeron JM, Aguadé M . An evaluation of measures of synonymous codon usage bias.. J. Mol. Evol. . 47 . 3 . 268–274 . 1998 . 9732453 . 10.1007/PL00006384. 1998JMolE..47..268C. 21862217.
4. Novembre J.A.. Accounting for background nucleotide composition when measuring codon usage bias.. Mol. Biol. Evol. . 19 . 8 . 1390–1394. 2002 . 12140252 . 10.1093/oxfordjournals.molbev.a004201. free .
5. Fuglsang A.. The 'effective number of codons' revisited.. Biochem. Biophys. Res. Commun. . 317 . 3 . 957–964 . 2004 . 15081433. 10.1016/j.bbrc.2004.03.138.
6. Marashi S.A. . Najafabadi H.S.. How reliable re-adjustment is: correspondence regarding A. Fuglsang, "The 'effective number of codons' revisited".. Biochem. Biophys. Res. Commun. . 324 . 1 . 1–2 . 2004 . 15464973. 10.1016/j.bbrc.2004.08.213.
7. Fuglsang A.. On the methodological weakness of 'the effective number of codons': a reply to Marashi and Najafabadi.. Biochem. Biophys. Res. Commun. . 327 . 1 . 1–3 . 2005 . 15629420. 10.1016/j.bbrc.2004.11.133 .
8. Banerjee T. . Gupta S.K. . Ghosh T.C.. Towards a resolution on the inherent methodological weakness of the "effective number of codons used by a gene".. Biochem. Biophys. Res. Commun. . 330 . 4 . 1015–8 . 2005 . 15823544. 10.1016/j.bbrc.2005.02.150.
9. Fuglsang A.. Estimating the "effective number of codons": the Wright way of determining codon homozygosity leads to superior estimates.. Genetics . 172 . 2 . 1301–7 . 2006 . 16299393. 10.1534/genetics.105.049643 . 1456227 .
10. Fuglsang A.. Accounting for background nucleotide composition when measuring codon usage bias: brilliant idea, difficult in practice.. Mol. Biol. Evol. . 23 . 7 . 1345–7 . 2006 . 16679346. 10.1093/molbev/msl009 . free .
11. Fuglsang A.. Impact of bias discrepancy and amino acid usage on estimates of the effective number of codons used in a gene, and a test for selection on codon usage.. Gene . 410 . 1 . 82–8 . 2008 . 18248919 . 10.1016/j.gene.2007.12.001 .