Effective number of codons

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 [cite journal |author=Wright F. |title=The 'effective number of codons' used in a gene. |journal=Gene |volume=87 |issue=1 |pages=23–29 |year=1990 |pmid=2110097 |doi=10.1016/0378-1119(90)90491-9] . The way that ENC is computed has obvious similarities to the computation of effective population size in population genetics [cite journal |author=Kimura, M. and Crow, J.F. |title=The number of alleles that can be maintained in a finite population.|journal=Genetics |volume=49 |pages=725–738 |year=1964 |pmid=14156929] . Although it is easy to compute ENC values, it has been shown that this measure is the one of the best measures to show Codon usage bias [cite journal |author=Comeron JM, Aguadé M. |title=An evaluation of measures of synonymous codon usage bias.|journal=J. Mol. Evol. |volume=47 |issue=3 |pages=268–274 |year=1998 |pmid=9732453 |doi=10.1007/PL00006384] .

Since the original suggestion of the ENC, several investigators have tried to improve the method [cite journal |author=Novembre J.A.|title=Accounting for background nucleotide composition when measuring codon usage bias.|journal=Mol. Biol. Evol. |volume=19 |issue=8 |pages=1390–1394|year=2002 |pmid=12140252] [cite journal |author=Fuglsang A.|title=The 'effective number of codons' revisited.|journal=Biochem. Biophys. Res. Commun. |volume=317 |issue=3 |pages=957–964 |year=2004 |pmid=15081433|doi=10.1016/j.bbrc.2004.03.138] , but it seems that there is much room to improve this measure [cite journal |author=Marashi S.A., Najafabadi H.S.|title=How reliable re-adjustment is: correspondence regarding A. Fuglsang, "The 'effective number of codons' revisited".|journal=Biochem. Biophys. Res. Commun. |volume=324 |issue=1 |pages=1–2 |year=2004 |pmid=15464973|doi=10.1016/j.bbrc.2004.08.213] [cite journal |author=Fuglsang A.|title=On the methodological weakness of 'the effective number of codons': a reply to Marashi and Najafabadi.
journal=Biochem. Biophys. Res. Commun. |volume=327 |issue=1 |pages=1–3 |year=2005 |pmid=15629420|doi=10.1016/j.bbrc.2004.11.133 ] [cite journal |author=Banerjee T., Gupta S.K., Ghosh T.C.|title=Towards a resolution on the inherent methodological weakness of the "effective number of codons used by a gene".|journal=Biochem. Biophys. Res. Commun. |volume=330 |issue=4 |pages=1015–8 |year=2005 |pmid=15823544|doi=10.1016/j.bbrc.2005.02.150] [cite journal |author=Fuglsang A.|title=Estimating the "effective number of codons": the Wright way of determining codon homozygosity leads to superior estimates.|journal=Genetics |volume=172 |issue=2 |pages=1301–7 |year=2006 |pmid=16299393|doi=10.1534/genetics.105.049643 ] [cite journal |author=Fuglsang A.|title=Accounting for background nucleotide composition when measuring codon usage bias: brilliant idea, difficult in practice.|journal=Mol. Biol. Evol. |volume=23 |issue=7 |pages=1345–7 |year=2006 |pmid=16679346|doi=10.1093/molbev/msl009 ] [cite journal |author=Fuglsang A.|title=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.|journal=Gene |volume=410 |issue=1 |pages=82–8 |year=2008 |pmid=18248919 ] .

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