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. [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]

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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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