Web-based design and evaluation of T-cell vaccine candidates |
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Authors: | Thurmond James Yoon Hyejin Kuiken Carla Yusim Karina Perkins Simon Theiler James Bhattacharya Tanmoy Korber Bette Fischer Will |
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Affiliation: | Los Alamos National Laboratory, Los Alamos, NM 87545, USA. |
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Abstract: | 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/. |
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