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OJB
Online Journal of Bioinformatics
Volume 19 (2):96-106, 2018.
Synonymous codon usage analysis of 32 mycobacteriophage
genomes.
Tuberculosis Research Centre, Chennai, India
ABSTRACT
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.
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