Small regions of preferential codon usage and their effect on overall codon bias--the case of the plp gene

Preferential codon usage within synonymous groups (codon bias), is hypothesised to be a consequence of either mutational pressure or translational selection. This paper examines PLP and DM-20, two transcripts differentially spliced from the plp gene, using a variety of previously described indices measuring codon bias as well as a novel index for quantifying the response to directional mutation pressure. The results demonstrate that small regions of extreme codon bias may have appreciable effects on the quantification of total bias, and that this effect may be either an increase or a decrease depending which index is used.