the characteristics of rare codon clusters in the genome and proteins of hepatitis c virus; a bioinformatics look

background recent studies suggest that rare codon clusters are functionally important for protein activity. methods here, for the first time we analyzed and reported rare codon clusters in hepatitis c virus (hcv) genome and then identified the location of these rare codon clusters in the structure of hcv protein. this analysis was performed using the sherlocc program that detects statistically relevant conserved rare codon clusters. results by this program, we identified the rare codon cluster in three regions of hcv genome; ns2, ns3, and ns5a coding sequence of hcv genome. for further understanding of the role of these rare codon clusters, we studied the location of these rare codon clusters and critical residues in the structure of ns2, ns3 and ns5a proteins. we identified some critical residues near or within rare codon clusters. it should be mentioned that characteristics of these critical residues such as location and situation of side chains are important in assurance of the hcv life cycle. conclusion the characteristics of these residues and their relative status showed that these rare codon clusters play an important role in proper folding of these proteins. thus, it is likely that these rare codon clusters may have an important role in the function of hcv proteins. this information is helpful in development of new avenues for vaccine and treatment protocols.