Many pathogenic organisms have an inherent ability to rapidly evolve into new variants, which enables them to escape previously existing immune responses. Vaccine design strategies should be aimed to counteract such variability, targeting the conserved antigen regions of the pathogen. Sequence variability analysis allows the identification of conserved regions upon multiple sequence alignments of the relevant antigens. In this chapter, we describe a detailed protocol and provide software to build variability-free proteomes for epitope-vaccine design. The procedure, which will be illustrated for human herpesvirus 1 (HHV1), involves the identification of protein clusters, followed by multiple sequence alignments and Shannon variability calculations. The software required to build variability-free proteomes is available at http://imed.med.ucm.es/software/mmb2019 .
Keywords: Clustering; Consensus sequence; Epitope; Multiple sequence alignments; Shannon entropy; Variability.