Fig. 1

The research outline of the study. The details can be found in the main text: Our analysis was based on coding sequences of 14 bacteriophages and 11 human viruses (A.), and on the ribo-seq measurements of bacteriophage Lambda and its E.coli host (B.). Basing on the existing literature, classification of the viral genes to early and late (with respect to the beginning of the lytic phase) was derived (C.). A., B., and C, were used to perform a comprehensive comparative genomics analysis of differential synonymous codon usage in early and late genes (D.), as well as of additional genomic features possibly related to codon bias (E.), such as: ribo-seq based codon typical decoding rates (TDR), Transfer Ribonucleic Acid (tRNA) adaptation indexes (tAI), effective number of codons (ENC), codon pairs bias (CPB), amino acids bias (AAB), dinucleotide bias (DNTB), nucleotide bias (NTB), GC content, number of genes in each temporary group and their length