The empirical codon mutation matrix as a communication channel

BMC Bioinformatics

Table 2 Calculated codon relative frequency

	Codon	Frequency	Codon	Frequency	Codon	Frequency	Codon	Frequency
T	TTT	0.0257	TCT	0.0113	TAT	0.0207	TGT	0.0215	T
	TTC	0.0264	TCC	0.0150	TAC	0.0260	TGC	0.0247	C
	TTA	0.0097	TCA	0.0100	TAA	*	TGA	*	A
	TTG	0.0119	TCG	0.0066	TAG	*	TGG	0.0439	G
C	CTT	0.0118	CCT	0.0159	CAT	0.0141	CGT	0.0073	T
	CTC	0.0150	CCC	0.0162	CAC	0.0183	CGC	0.0129	C
	CTA	0.0054	CCA	0.0161	CAA	0.0144	CGA	0.0077	A
	CTG	0.0277	CCG	0.0085	CAG	0.0337	CGG	0.0065	G
A	ATT	0.0162	ACT	0.0071	AAT	0.0160	AGT	0.0130	T
	ATC	0.0205	ACC	0.0128	AAC	0.0212	AGC	0.0163	C
	ATA	0.0088	ACA	0.0093	AAA	0.0251	AGA	0.0157	A
	ATG	0.0330	ACG	0.0079	AAG	0.0261	AGG	0.0122	G
G	GTT	0.0096	GCT	0.0132	GAT	0.0234	GGT	0.0114	T
	GTC	0.0114	GCC	0.0172	GAC	0.0228	GGC	0.0162	C
	GTA	0.0060	GCA	0.0110	GAA	0.0235	GGA	0.0183	A
	GTG	0.0260	GCG	0.0048	GAG	0.0263	GGG	0.0126	G
	T		C		A		G

The codon relative frequency that maximizes the mutual information between input and output and yielding a capacity close to what is required for preserving the information content of amino acids. An exponential factor of 0.26 is applied to the ECM matrix.

ISSN: 1471-2105