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Bioinformatics Advance Access published online on May 29, 2008
Bioinformatics, 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,*, Hyejin Yoon 1,*, Carla Kuiken 1, Karina Yusim 1, Simon Perkins 2, James Theiler 1, Tanmoy Bhattacharya 1,3, Bette Korber 1,3 and Will Fischer 1,{dagger}

1Los Alamos National Laboratory, Los Alamos, NM 87545.
2UltraSpectral Inc., 5701 Carmel Ave. NE, Suite C, Albuquerque NM 87113.
3The Santa Fe Institute, Santa Fe, NM 87501

{dagger} To whom correspondence should be addressed. Will Fischer, E-mail: wfischer{at}lanl.gov, btk{at}lanl.gov


  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/.../http://www.hiv.lanl.gov/content/sequence/MOSAIC/makeVaccine.html, .../http://www.hiv.lanl.gov/content/sequence/MOSAIC/epicover.html, .../http://www.hiv.lanl.gov/content/sequence/MOSAIC/posicover.html.

Contact: wfischer{at}lanl.gov, btk{at}lanl.gov

Supplementary Data: ftp-t10.lanl.gov/~btk/WebToolsData

Associate Editor: Prof. Alfonso Valencia

* These authors contributed equally to this work.

Received on January 7, 2008; revised on May 8, 2008; accepted on May 28, 2008

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