Analysis of synonymous codon usage bias, nucleotide and amino acid composition in 13 species of Flaviviridae

Flaviviridae are viruses that cause several diseases including Dengue fever, Japanese encephalitis, Murray Valley encephalitis, Tick-borne encephalitis, West Nile encephalitis, Yellow fever and Hepatitis C Virus Infection. Members of this family have monopartite, linear, single-stranded RNA genomes of positive polarity, 9.6-12.3 kb in length. Here, we have analyzed the codon usage of 13 species of this family by using gene infinity pakage. Base and amino acid composition analysis was also performed by CAIcal server and PseAAC web-sever respectively. The results showed that the highest number of A, G and C bases were seen in the RNA genome of Dengue virus 2, Tick borne encephalitis virus and Hepatitis C virus respectively. Although the number of U base used in RNA genomes was very close, the highest U nucleotide amount was 23.77% in Wesselsbron virus. The lowest number of C, G, U and A bases was seen in Bovine viral diarrhea virus, Dengue virus 2, Tick borne encephalitis virus and Hepatitis C virus respectively. In this study, it is found that the complete genome of classical swine fever virus has a lower GC content and genome of Tick borne encephalitis virus, Hepatitis C virus and Powassan virus have a higher GC content than other species. We also classified the amino acids as rare (Phenylalanine, Cysteine, Histidine, Methionine, Asparagine, Glutamine, Tryptophan and Tyrosine), frequent (Alanine, Glutamic acid, Glycine, Leucine, Valine and Threonine), and intermediate (all others). The highest and the lowest number of preferred codons exist in Wesselsbron virus and West Nile virus, respectively.