Estimating the "effective number of codons": the Wright way of determining codon homozygosity leads to superior estimates.

ABSTRACT: In 1990, Frank Wright introduced a method for measuring synonymous codon usage bias in a gene by estimation of the "effective number of codons," N(c). Several attempts have been made recently to improve Wright's estimate of N(c), but the methods that work in cases where a gene encodes a protein not containing all amino acids with degenerate codons have not been tested against each other. In this article I derive five new estimators of N(c) and test them together with the two published estimators, using resampling under rigorous testing conditions. Estimation of codon homozygosity, F, turns out to be a key to the estimation of N(c). F can be estimated in two closely related ways, corresponding to sampling with or without replacement, the latter being what Wright used. The N(c) methods that

SUBMITTER: Fuglsang A 

PROVIDER: S-EPMC1456227 | biostudies-literature | 2006 Feb

REPOSITORIES: biostudies-literature