Dependency of codon usage on protein sequence patterns: a statistical study

Table 1 Percentages of the patterns for which the pattern codon usage is not random

Amino acid	Number of codons for amino acid	Number of valid patterns	Number of patterns with non-random codon usage in pattern region	Percentages of patterns with non-random codon usage in pattern region
C	2	24	15	%62.5
D	2	43	29	%67.4
E	2	41	25	%61.0
F	2	40	27	%67.5
H	2	33	16	%48.5
K	2	35	21	%60.0
N	2	38	15	%39.5
Q	2	38	22	%57.9
Y	2	37	15	%40.5
I	3	52	48	%92.3
A	4	47	45	%95.7
G	4	54	46	%85.2
P	4	38	34	%89.5
T	4	48	42	%87.5
V	4	56	47	%83.9
L	6	50	49	%98.0
R	6	34	33	%97.1
S	6	40	39	%97.5

We excluded amino acids with exactly one codon. If an amino acid appears 10 times in a pattern region, and each of its codons appears at least once in this region, we consider the pattern as a valid pattern for the amino acid. A pattern with non-random codon usage is a pattern for which the randomness hypothesis with respect to a completely random background is rejected.

ISSN: 1742-4682