Increased incidence of rare codon clusters at 5' and 3' gene termini: implications for function

BMC Genomics

Table 1 The population of rare codon clusters is markedly higher at the termini relative to the non-terminal positions

	Percent of genes with rare codon clusters^a
	5'	Non-terminal average	3'
E. coli	8.49 *	2.35 ± 0.32	4.60 *
A. tumefaciens	9.44 *	0.96 ± 0.24	2.87 *
B. anthracis	1.08	0.47 ± 0.15	1.03
B. cereus	1.21	0.60 ± 0.16	1.33
B. fragilis	5.68	3.52 ± 0.37	4.10
B. subtilis	4.83	4.04 ± 0.37	5.08
B. pertussis	2.01 *	0.14 ± 0.06	0.65 *
B. melitensis 16 M	9.97 *	0.86 ± 0.21	3.49 *
Burkholderia sp. 383	1.97 *	0.36 ± 0.09	0.72
C. burnetii	0.55	0.26 ± 0.17	0.55
C. neoformans	11.12	11.06 ± 1.10	21.24 *
D. radiodurans	4.54 *	0.92 ± 0.20	2.27
E. carotovora	10.28 *	3.59 ± 0.42	6.62 *
H. pylori	1.64	0.73 ± 0.31	0.88
N. meningitidis	4.69	2.45 ± 0.63	4.59
Nostoc sp. PCC 7120	4.22	2.39 ± 0.30	4.26
P. fluorescens	3.86 *	0.85 ± 0.16	2.11 *
R. metallidurans CH34	2.77 *	0.57 ± 0.14	2.13 *
S. entericia	8.49 *	2.47 ± 0.29	4.90
S. typhimurium	8.70 *	2.55 ± 0.32	5.19 *
S. flexneri	8.28 *	2.63 ± 0.65	6.12
S. meliloti	2.72 *	0.42 ± 0.11	1.76 *
S. aureus	0.64	0.16 ± 0.11	0.56
T. thermophilus	0.73	0.25 ± 0.14	2.02 *
X. fastidiosa	7.76 *	3.21 ± 0.63	5.85
Y. pestis	9.66 *	3.18 ± 0.83	7.54

^a5' and 3' values that are greater than 7 standard deviations from the average of the non-terminal positions are denoted with an asterisk (*).

ISSN: 1471-2164