Effective number of codons

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]}

References

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