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).