Bioinformatics Advance Access originally published online on May 29, 2008
Bioinformatics 2008 24(14):1639-1640; doi:10.1093/bioinformatics/btn251
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Web-based design and evaluation of T-cell vaccine candidates


1Los Alamos National Laboratory, Los Alamos, NM 87545, 2UltraSpectral Inc., 5701 Carmel Ave. NE, Suite C, Albuquerque NM 87113 and 3The Santa Fe Institute, Santa Fe, NM 87501, USA
*To whom correspondence should be addressed.
| Abstract |
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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{at}lanl.gov
Supplementary information: Supplementary data are available at ftp://ftp-t10.lanl.gov/pub/btk/WebToolsData
Associate Editor: Alfonso Valencia
The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.
Received on January 7, 2008; revised on May 8, 2008; accepted on May 28, 2008
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