Strategies for vaccine design for corona virus using Immunoinformatics techniques

Anamika Basu; Anasua Sarkar; Ujjwal Maulik

The protein family information of Coronavirus nonstructural protein NS4 containing 78 protein is retrieved from InterPro database (https://www.ebi.ac.uk/interpro/entry/InterPro/IPR005603/). To find conserved region, retrieved sequences were aligned using Muscle tool 3.8.31 [8] where k-mer clustering is used. In the next step a phylogenetic tree is constructed by the method known as progressive alignment. The evolutionary divergence analysis for all 78 virus proteins are completed by forming a phylogenetic tree using Phy ML 3.1/3.0 aLRT software [9] . Here the phylogenetic tree was reconstructed using the maximum likelihood method. The default substitution model was selected assuming an estimated proportional of invariant sites (of 0.008) and 4 gammadistributed rate categorized to account for rate heterogenicity across sites. The gamma shape parameter was estimated directly from the data (gamma = 1.788). Reliability for internal branch was assessed using the aLRT test (SH-like).