In Silico Comparison of Synonymous Codons Usage between the Coding Sequences of Low and High Risk

Human papillomaviruses (HPVs) are small non-enveloped viruses with a a double-stranded DNA. The genome of HPVs encodes a number of early and late proteins. These viruses can be classified into high risk and low risk groups according to production of malignant lesions. In the present study، we analyzed the synonymous codon usage in coding sequences of high and low risk human papillomavirus genomes. The synonymous codon usage of these two groups was obtained from http: //www. kazusa. or. jp/codon and analyzed using the ROC software. Statistical data analysis indicated that the usage of five codons of UAU (tyrosin)، UGU (cysteine)، ACA (threonine)، AGG (argenine)، and GUC (valine) was significantly different between high and low types. The results of our study revealed the usefulness of codon usage analysis for the classification of high and low risk human papillomavirus.