Unbiased estimation of symmetrical directional mutation pressure from protein-coding DNA

The most generally applicable procedure for obtaining estimates of the symmetrical, or strand-nonspecific, directional mutation pressure (μ(D)) on protein-coding DNA sequences is to determine the G+C content at synonymous codon sites (P(syn)), and to divide P(syn) by twice the arithmetic mean of the G+C content at synonymous codon sites of a large number of randomly generated, synonymously coding DNA sequences (P̄(syn)). Unfortunately, the original procedure yields biased estimates of P(syn) and μ(D) and is computationally expensive. We here present a fast procedure for estimating unbiased μ(D) values. The procedure employs direct calculation of P(circumflex)(syn) (≃P̄(syn)) and two normalization procedures, one for P(syn) ≥ P(circumflex)(syn) and another for P(syn) ≥ P(circumflex)(syn). The normalization removes a bias sometimes caused by codons specifying arginine, asparagine, isoleucine, and leucine. Consequently, comparison of protein-coding genes that are translated using different genetic codes is facilitated.