Comput Biol Chem - A more accurate relationship between 'effective number of codons' and GC3s under assumptions of no selection.

Tópicos

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Resumo

The 'effective number of codons' (Nc) introduced by Frank Wright in 1990 is one of the best measures to show the state of codon usage biases in genes and genomes. Although estimate methods of Nc have been improved by several investigators since then, no one noticed that the relationship between Nc and GC3s under assumptions of no selection given by Wright has a little but significant deviation. Since the curve showing such a relationship in Nc-plot is a useful reference line to display the main features of codon usage pattern for a number of genes, its high accuracy is important and necessary. Under ideal and ultimate conditions listed in this text a computational sample of Nc versus GC3s was derived and calculated. By nonlinear regression analysis, the relationship between Nc and GC3s without synonymous codon selection can be approximated by: N(c)=2.5-s+29.5/(s(2)+(1-s)(2)), instead of Wright's: N(c)=2+s+29/(s(2)+(1-s)(2)), where s denotes GC3s. The goodness of fit analysis of both confirmed that the new formula presented in this text is more accurate than the original one. In addition, in the case of using the same estimate method of Nc, the situation in overestimation is decreased to a certain extent by using the new reference line in comparison with Wright's one.

Resumo Limpo

effect number codon nc introduc frank wright one best measur show state codon usag bias gene genom although estim method nc improv sever investig sinc one notic relationship nc gcs assumpt select given wright littl signific deviat sinc curv show relationship ncplot use refer line display main featur codon usag pattern number gene high accuraci import necessari ideal ultim condit list text comput sampl nc versus gcs deriv calcul nonlinear regress analysi relationship nc gcs without synonym codon select can approxim ncsss instead wright ncsss s denot gcs good fit analysi confirm new formula present text accur origin one addit case use estim method nc situat overestim decreas certain extent use new refer line comparison wright one

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