Similar protocols

Pipeline publication

[…] wo different types of proteins was retrieved from BioEdit tool through ClustalW with 1,000 bootstrap replicates (Figures S1 and S2). Conserved regions were grouped for the antigenic property analysis. CLC Sequence Viewer was used to construct phylograms for both proteins from the MSA obtained from BioEdit, in order to analyze the divergence among the retrieved sequences. Phylogram of RNA-dependent RNA polymerase-L is depicted in and the phylogram for the envelope glycoprotein is provided in Figure S3., Initially, the conserved sequences (MSA number: 3,563–3,915) of RNA-dependent RNA polymerase-L were separated into four conserved peptides, according to their continuity in the MSA. Then the VaxiJen v2.0 server was used to predict the antigenicity of all the grouped conserved peptides (). On the basis of the VaxiJen score, the top two conserved peptides (MSA number: 3,563–3,658 and 3,694–3,773) were selected for further analysis. The peptide with second-best VaxiJen score (MSA: 3,694–3,773) showed better results during further analysis of T-cell epitope identification, MHC interaction analysis, and B-cell epitope identification. The conservancy of this region among the different viral strains is partially depicted in ., NetCTL v1.2 server predicted the T-cell epitopes through the combined approach for the 12 MHC-I supertypes. On the basis of the combined score, five epitopes with top scores () were selected for further analysis. CTLPred server also predicted the T-cell epitopes based on an approach that combined artificial neural networks and support vector machines (). From the analysis, the common epitope–containing peptide, which was predicted by both servers, was selected and used for the MHC-binding analysis., MHC-I-binding prediction, which was run through the Stabilized Matrix Method, predicted a wide range of MHC-I allele interactions for the proposed T-cell epitopes. The MHC-I alleles for which the epitope showed higher affinity (IC50 <200 nM) are listed in . The output of the MHC-II interaction analysis is also shown in ., Amino acid–based methods were used for the prediction of potential B-cell epitope […]

Pipeline specifications

Software tools VaxiJen, NetCTL, CTLPred