A comparative analysis of codon usage and CAI in hsv-۱ and hsv-۲

BACKGROUND AND OBJECTIVESGlycoprotein D in herpes simplex viruses is involved in binding to the receptor of host cells and the process of entering the cell.MATERIALS AND METHODSIn this study, the glycoprotein D gene was investigated in two human herpes simplex viruses type ۱ and ۲ using the http://genomes.urv.cat/CAIcal server. First, by extracting the sequence of gD genes from the NCBI database, the coding sequence (CDS) of these genes was identified and selected, then these two sequences were used as raw data for the various sections of the mentioned server. The standard codon usage table and human codon usage were used as reference sets. Using these two sequences, different components such as sequence length, nucleotide composition, codon usage, and Relative Synonymous Codon Usage (RSCU) were calculated.RESULTS AND DISCUSSIONThese investigations showed that according to the sequence length and similar G+C percentage, in each of the viruses, some codons of amino acids may be used more, and some codons may never be used. codon UUA (leucine) and codon GGU (glycine) in HSV-۱ and codon UCA (proline), codon CCU (cysteine) and codon AGG (arginine) in HSV-۲, as well as codon AGA (arginine) in both viruses to make Glycoprotein D have never been used and has ۰% codon usage. Among the translation termination codons in both types of viruses, only the UAG codon is used. In another option of the server, which was related to the calculation of codon adaptation index (CAI), two parameters CAI and expected CAI were calculated. eCAI provides a direct threshold value that makes it possible to discern whether differences in the CAI value are statistically significant or merely artifacts arising from internal biases in the G+C composition and/or the amino acid composition of the query sequences. The CAI of the sequences is equal to ۰.۷۹۲ and ۰.۷۵۷ for HSV۱- and HSV-۲, respectively. And the expected CAI (eCAI) for these sequences is ۰.۸۰۴ at the ۹۵% confidence level and ۰.۸۳۶ at the ۹۹% confidence level.CONCLUSIONThis shows that the CAI of both sequences is not significantly higher than the expected CAI at both confidence levels due to their nucleotide and amino acid composition.

کلیدواژه ها:

Herpes simplex viruses ، gD glycoprotein ، CAIcal server ، Codon usage