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Effective number of codons

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Effective number of codons (abbreviated as ENC or Nc) is a measure to study the state of codon usage biases in genes and genomes. The way that ENC is computed has obvious similarities to the computation of effective population size in population genetics. 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.

Since the original suggestion of the ENC, several investigators have tried to improve the method, but it seems that there is much room to improve this measure.

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. & Crow, J.F. (1964). "The number of alleles that can be maintained in a finite population". Genetics. 49 (4): 725–738. doi:10.1093/genetics/49.4.725. 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. Bibcode:1998JMolE..47..268C. doi:10.1007/PL00006384. PMID 9732453. S2CID 21862217.
  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.


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