The three tools that make up this suite allow users to design and assess vaccine candidate protein sequences. The vaccine design tool uses the mosaic method to generate protein sequences optimized to include a high proportion of immunological epitopes; the assessment tools let users compare epitope 'coverage' for any group of potential antigens.
These tools are meant to be user-friendly. Try the 'Sample Input' provided with each tool to see a demonstration. The tools in this suite were designed to be used in order, but the assessment tools can be used with any 'vaccine' and background sequence set. The tools can be used independently, so results can be analyzed whenever it is convenient. The results page for the Vaccine Designer tool provides links that let you transfer the data from that set of results directly to either of the assessment tools.
You may wish to read the Mosaic Explanation file to familiarize yourself with the techniques . The references cited below provide additional details.
Mosaic Vaccine Designer: The Mosaic Vaccine Designer will generate candidate vaccine protein 'cocktails' that optimize coverage of potential T-cell epitopes found in a given background set of protein sequences. The resulting 'mosaic' proteins in the proposed vaccine cocktail resemble real proteins from the input set of natural viral proteins (the 'training set'), but are assembled from fragments of the natural proteins using a genetic algorithm (a computational optimization method), in a way that prevents formation of new epitopes. For more details, see Mosaic Explanation.
Epitope Coverage Assessment: Given a potential vaccine or antigen protein 'cocktail', and a set of natural or background proteins, this tool will calculate the fraction of all of the epitope-length peptides in the test sequence set that are 'covered' (i.e., matched) by some peptide in each protein cocktail. Tables and graphs (see examples below) representing this coverage are generated. Coverage can be calculated for various subsets of the background protein sequences. Results are expressed as mean epitope-coverage over all background sequences.
Positional Epitope Coverage Assessment: Given a potential vaccine or antigen protein 'cocktail', and an alignment of natural or background proteins, this tool generates graphics (see examples below) showing various aspects of epitope coverage by alignment position and by degree of coverage. This tool will calculate the fraction of all of the epitope-length peptides in a set of aligned viral or antigen protein sequences that are 'covered' (i.e., matched) by some peptide in the viral or antigen protein cocktail. Results are expressed as epitope-coverage over the position of test sequences.