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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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© The Author 2008. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

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

James Thurmond 1,{dagger}, Hyejin Yoon 1,{dagger}, Carla Kuiken 1, Karina Yusim 1, Simon Perkins 2, James Theiler 1, Tanmoy Bhattacharya 1,3, Bette Korber 1,3 and Will Fischer 1,*

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

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

{dagger}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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