The number of those amino acids that are encoded by the same codon (c) was determined, and the fraction (f2 = c/ n) of the codons that are the same were then tabulated (Supplementary Table [see Additional File 2]).
For amino acids with amino acid precursors, we have: (i) 0 of these are codified by GNN codons (= c), and (ii) 14 of these are codified by non-GNN codons (= d).
For example, codon c is read by tRNA i that can read four codons.
Codon c can also be read by another tRNA that reads three codons.
In the following, stands for the probability of the event codon c i mutates into codon c j in evolutionary time θ, and is given by a codon substitution probability matrix.
For the total genes group, the optimal codons all ended by G or C, and all amino acids excluding Met and Trp were identified by different numbers of codons.
A predicted extension was scored positively if: (a) there existed ribosome density in the extension, (b) ribosome density vanished or unambiguously decreased after the extension's in-frame stop codon, and (c) positions occupied by ribosomes in the readthrough region were evenly-spaced throughout the extension.
One may propose an alternative hypothesis for the observation that NNY codon families are translated by tRNAs with a wobble G whereas NNR codon families translated by tRNAs with a wobble C and a wobble U, respectively.
There are four known genes encoded by the genome, called C, X, P, and S. The core protein is coded for by gene C (HBcAg), and its start codon is preceded by an upstream in-frame AUG start codon from which the pre-core protein is produced.
We ran three variant analyses, one with all the data unpartitioned, a second with the data partitioned by codon position (a "codon" partitioning scheme, with rDNA genes considered as additional data partitions), and a third with the data partitioned by both gene and codon positions ("G×C," or gene by codon partitioning); see below for how the final partitioning schemes were set up.
