Relative synonymous codon usage (RSCU) analysis
Relative synonymous codon usage (RSCU) is a measure for assessing the
uneven use of synonymous codons in nucleotide sequences or in the genome
and is calculated using equation (4):
\(RSCU=\ \frac{X_{i}}{\left(\frac{1}{n}\right)\sum_{i=1}^{n}X_{i}}\) (4),
where n is the number of synonymous codons for the X -amino
acid (1 ≤ n ≤ 6); Xi is the number of
occurrences of the i -codon in the nucleotide sequence. Codons
with RSCU > 1 are considered as frequent, and a higher RSCU
corresponds to a larger bias in codon usage. RSCU < 1
indicates the opposite situation. If the RSCU is one, no codon usage
bias is observed. The latter corresponds to the Met and Trp residues,
since these amino acids have no synonymous codons in accordance with the
standard genetic code (Supplementary, Genetic Code).
In this work, RSCU values were determined for each nucleotide sequences
from database 2. Average RSCU values were determined for 17 phyla,
excluding Viruses and Platyhelminthes (Supplementary, RSCU).