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Synonymous codon usage bias in 16 Staphylococcus aureus phages: implication in phage therapy.

Sau K, Gupta SK, Sau S, Ghosh TC

Bioinformatics Centre, Bose Institute, P1/12, CIT Scheme VII M, Calcutta 700 054, India. sau@bic.boseinst.ernet.in

To reveal the factors influencing architecture of protein-coding genes in staphylococcal phages, relative synonymous codon usage variation has been investigated in 920 protein-coding genes of 16 staphylococcal phages. As expected for AT rich genomes, there are predominantly A and T ending codons in all 16 phages. Both Nc plot and correspondence analysis on relative synonymous codon usage indicates that mutation bias influences codon usage variation in the 16 phages. Correspondence analysis also suggests that translational selection and gene length also influence the codon usage variation in the phages to some extent and codon usage in staphylococcal phages is phage-specific but not S. aureus-specific. Further analysis indicates that among 16 staphylococcal phages, 44AHJD, P68 and K may be extremely virulent in nature as most of their genes have high translation efficiency. If this is true, then above three phages may be useful for curing staphylococcal infections.

Published 26 September 2005 in Virus Res, 113(2): 123-31.
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