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Online Journal of Bioinformatics

Volume 19 (2):96-106, 2018.

Synonymous codon usage analysis of 32 mycobacteriophage genomes.


Sameer Hassan, Vasantha Mahalingam, Vanaja Kumar.


Tuberculosis Research Centre, Chennai, India




Hassan S, Mahalingam V, Kumar V., Synonymous codon usage analysis of 32 mycobacteriophage genomes, Onl J Bioinform., 19 (2):96-106, 2018. Modification of codons of the luciferase gene with respect to optimal codons of the phage and the host could lead to better expression of the gene to improve the sensitivity of mycobacterial detection by luciferase reporter phage assay. We describe codon usage patterns of all the mycobacteriophages so far sequenced to optimize luciferase phage assay. Synonymous codon usage of protein coding genes of 32 completely sequenced mycobacteriophage genomes was determined by multivariate statistical analysis. One of the major factors influencing codon usage is compositional bias in highly expressed genes wherein codons ending in C are highly preferred over those ending in G. Translational selection shapes codon usage and translational accuracy. High level of heterogeneity was found amongst, and between the genomes. Length of genes influenced codon usage in 14 out of 32 phage genomes in a minor way. Mycobacteriophage Cooper was found to be a highly biased genome with better translation efficiency comparing well with the host specific tRNA genes.


Key words: Synonymous codons, translational selection, mutational bias, Nc, GC3s. Synonymous codon usage analysis of 32 mycobacteriophage genomes.