The family, Flaviviridae includes viruses which 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 with 9.6-12.3 kb in length. Here, we analyzed the codon usage of 13 species of this family by
using gene infinity package. Base analysis was performed by CAIcal server and amino acid composition was
calculated by PseAAC web-server. 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 bases 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 was
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 the highest GC content among other
examined 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 numbers of preferred codons exist in Wesselsbron
virus and the lowest in West Nile virus. |
