Sentence examples for mixed codons used from inspiring English sources
Fig. 11 shows a compilation of the more common types of mixed codons used.
Additionally, according to the codon usage table of L. lactis subsp. cremoris MG1363 (Additional file 5) an analysis of usage of the first 50 codons of the complete ORF and dkr gene, shows that 10 codons (ORF) and 8 codons (dkr), respectively can be considered "rare codons" (i.e. codons used in less than 20% of the cases) or "very rare codons" (i.e. codons used in less than 10% of the cases).
The codons used in less than 20% of the cases are considered as rare and their codon usage fraction appears in grey.
As the approximate index of optimum codons, we used preferred codons, or most frequently used codon for an amino acid, and evaluated the preferred codon fraction in SCCSs.
Fop is the ratio of optimal codons to synonymous codons, ranging from 0 (where no optimal codons are used) to 1 (where only optimal codons are used).
Codon usage bias indicates that specific codons are used more often from other synonymous codons by gene translation.
Along similar lines, Baranov et al. [ 81] have stated that "the emerging picture of decoding strategies used by different organisms...argue [sic] that non-triplet codes or codes with mixed codon sizes are possible"; further, they have provided evidence from computer modelling that decoding systems with codons larger than three nucleotides evolve spontaneously into mainly triplet decoding systems.
Altogether, the emerging picture of decoding strategies used by different organisms, besides possibilities to artificially manipulate the genetic code, argue that non-triplet codes or codes with mixed codon sizes are possible.
Codon optimization was performed by choosing only codons preferentially used in humans and with over 60% GC content, and the method was named the "preferred human codon-optimized method".
