Web-based design and evaluation of T-cell vaccine candidates

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Abstract
Summary: We present a suite of on-line tools to design candidate vaccine proteins, and to assess antigen potential, using coverage of k-mers (as proxies for potential T-cell epitopes) as a metric. The vaccine design tool uses the recently published ‘mosaic’ method to generate protein sequences optimized for coverage of high-frequency k-mers; the coverage-assessment tools facilitate coverage comparisons for any potential antigens. To demonstrate these tools, we designed mosaic protein sets for B-clade HIV-1 Gag, Pol and Nef, and compared them to antigens used in a recent human vaccine trial. Availability: http://hiv.lanl.gov/content/sequence/MOSAIC/ Contact: wfischer@lanl.gov Supplementary information: Supplementary data are available at ftp://ftp-t10.lanl.gov/pub/btk/WebToolsData