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Alfalfa mosaic virus (AMV) infects over 600 plant species in 70 families (experimental and natural hosts). Coat proteins are important materials for making structure-function correlations with biologically active peptides on the physicochemical and immunochemical levels and also are good models for observing the evolutional changes in protein molecules. Antigenic peptides at position 1-MSSSQKKAGGKAGKPTKRSQN-21; 151-PTHAGMQNQNF-161; 22-YAALRKAQLPKPPALKVPVVKPT-44 of Alfalfa mosaic virus coat protein are most suitable for subunit vaccine development because with single epitope, the immune response can be generated in large population. In this research, we used PSSM and SVM algorithms for the prediction of MHC class I & II binding peptide, antigenicity, Solvent accessibility, polar and nonpolar residue to analyse the regions that are likely exposed on the surface of proteins which are potentially antigenic that allows potential drug targets to identify active sites against infection as well as to design synthetic peptide vaccine.
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