A new measure for assessing codon bias of one group of genes with respect to a 
second group of genes is introduced. In this formulation, codon bias 
correlations for Escherichia coli genes are evaluated for level of expression, 
for contrasts along genes, for genes in different 200 kb (or longer) contigs 
around the genome, for effects of gene size, for variation over different 
function classes, for codon bias in relation to possible lateral transfer and 
for dicodon bias for some gene classes. Among the function classes, codon biases 
of ribosomal proteins are the most deviant from the codon frequencies of the 
average E. coli gene. Other classes of 'highly expressed genes' (e.g. amino acyl 
tRNA synthetases, chaperonins, modification genes essential to translation 
activities) show less extreme codon biases. Consistently for genes with 
experimentally determined expression rates in the exponential growth phase, 
those of highest molar abundances are more deviant from the average gene codon 
frequencies and are more similar in codon frequencies to the average ribosomal 
protein gene. Independent of gene size, the codon biases in the 5' third of 
genes deviate by more than a factor of two from those in the middle and 3' 
thirds. In this context, there appear to be conflicting selection pressures 
imposed by the constraints of ribosomal binding, or more generally the early 
phase of protein synthesis (about the first 50 codons) may be more biased than 
the complete nascent polypeptide. In partitioning the E. coli genome into 10 
equal lengths, pronounced differences in codon site 3 G+C frequencies 
accumulate. Genes near to oriC have 5% greater codon site 3 G+C frequencies than 
do genes from the ter region. This difference also is observed between small 
(100-300 codons) and large (>800 codons) genes. This result contrasts with that 
for eukaryotic genomes (including human, Caenorhabditis elegans and yeast) where 
long genes tend to have site 3 more AT rich than short genes. Many of the above 
results are special for E. coli genes and do not apply to genes of most 
bacterial genomes. A gene is defined as alien (possibly horizontally 
transferred) if its codon bias relative to the average gene exceeds a high 
threshold and the codon bias relative to ribosomal proteins is also 
appropriately high. These are identified, including four clusters (operons). The 
bulk of these genes have no known function.