Table 1. Codon frequency (CF) for E. coli highly expressed genes (HEGs) and non-HEGs, as well as the computed S_i values according to Equation 1.

AA	Codon	CFHEGa	CFnon-HEGb	Si
A	GCA	1973	25,511	1.1495
A	GCG	2654	43,261	0.9118
A	GCC	1306	33,463	0.5646
A	GCU	2288	18,526	1.7865
C	UGC	475	8,397	1.1541
C	UGU	270	6,802	0.8098
D	GAC	2786	23,226	1.5125
D	GAU	2345	41,472	0.7130
E	GAA	4683	49,154	1.1180
E	GAG	1459	22,920	0.7470
F	UUC	2229	20,332	1.7637
F	UUU	872	29,556	0.4746
G	GGA	118	10,786	0.7282
G	GGG	267	14,842	1.1975
G	GGC	2987	37,418	0.8210
G	GGU	3583	30,154	1.2221
H	CAC	1160	12,144	1.7105
H	CAU	477	17,170	0.4975
I	AUA	22	5,926	0.0000
I	AUC	3488	30,787	1.5592
I	AUU	1640	39,788	0.5673
K	AAA	4129	41,696	1.0469
K	AAG	1050	13,057	0.8502
L	CUA	54	5,258	0.1275
L	CUG	5698	66,130	1.0694
L	CUC	541	14,591	1.2085
L	CUU	357	14,679	0.7927
L	UUA	210	18,739	0.7639
L	UUG	333	18,273	1.2422
M	AUG	2444	35,527	0.0000
N	AAC	2832	26,674	1.5850
N	AAU	539	23,652	0.3402
P	CCA	474	11,046	0.5779
P	CCG	2509	29,125	1.1601
P	CCC	38	7,443	0.2235
P	CCU	343	9,235	1.6258
Q	CAA	550	20,405	0.4975
Q	CAG	2548	36,780	1.2788
R	AGA	21	2,880	0.9782
R	AGG	13	1,681	1.0374
R	CGA	34	4,837	1.2807
R	CGG	33	7,370	0.8158
R	CGC	1530	28,473	0.6413
R	CGU	2995	25,528	1.4001
S	AGC	1015	20,868	1.3432
S	AGU	168	11,802	0.3931
S	UCA	189	9,614	0.9119
S	UCG	275	11,909	1.0711
S	UCC	1110	10,649	0.8950
S	UCU	1320	10,217	1.1094
T	ACA	181	9,527	0.7719
T	ACG	526	19,197	1.1132
T	ACC	2533	29,335	0.9108
T	ACU	1286	10,950	1.2389
V	GUA	1329	13,513	1.5053
V	GUG	1784	34,133	0.8000
V	GUC	824	19,972	0.4993
V	GUU	2669	22,297	1.4485
W	UGG	819	19,945	0.0000
Y	UAC	1569	15,094	1.5503
Y	UAU	865	21,207	0.6083

^aTaken from the Ecoli_high.cut file distributed with EMBOSS 6.4 (Rice et al. 2000) representing a compilation of codon usage from known highly expressed E. coli K12 genes.

^bMean codon frequencies from four sequenced E. coli K12 genomes (NC_010473, NC_020518, NC_007779, and NC_000913) minus CF_HEG.