Quantification of codon selection for comparative bacterial genomics

BMC Genomics

Table 2 Correlation of codon statistics with rates of sequence divergence.

			Pearson correlation of codon statistic with dS
Reference Genome ¹	Target Genome	Mean dS ²	ACE _u	CAI	E	MELP	GCB	RF³
B. subtilis 168	B. subtilis W23	0.24	-0.20	-0.18	-0.25	-0.22	-0.20	0.12
P. aeruginosa PA01	P. aeruginosa PA7	0.43	-0.23	-0.18	-0.18	-0.22	-0.23	0.13
E. coli K12	E. fergusonii	0.5	-0.29	-0.30	-0.26	-0.22	-0.29	0.15
L. gasseri	L. johnsonii	0.87	-0.56	-0.48	-0.65	-0.60	-0.56	0.41
S. haemolyticus	S. lugdensis	0.95	-0.48	-0.45	-0.47	-0.47	-0.48	0.19
E. coli K12	S. enterica	0.98	-0.51	-0.49	-0.61	-0.57	-0.51	0.26
B. amyloliquifaciens	B. subtilis W23	1.04	-0.51	-0.44	-0.54	-0.52	-0.50	0.32
P. aeruginosa PA01	P. mendocina	1.17	-0.59	-0.14	-0.58	-0.60	-0.59	0.40

1. Genome from which codon bias statistics were calculated. All codon statistics were calculated using the Translation40 gene set to construct f_o and all ORFs to construct f_n.
2. Average divergence (dS) and correlation were measured among putative orthologs with dS < 1.5 between reference and target genomes.
3. Correlation to log(probability) of belonging to the core genome as classified by Random Forest classifier [11]; RF values were calculated from a forest of 1000 trees as reported by Supek et al. [11].

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