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


BACKGROUND
http://hiv.lanl.gov/content/sequence/MOSAIC/.
Los Alamos National Laboratory, Los Alamos, NM 87545, USA.
James
J
Thurmond
Hyejin
H
Yoon
Carla
C
Kuiken
Karina
K
Yusim
Simon
S
Perkins
James
J
Theiler
Tanmoy
T
Bhattacharya
Bette
B
Korber
Will
W
Fischer
D016915:AIDS Vaccines / Q000737:chemistry*; D000465:Algorithms; D000941:Antigens / Q000737:chemistry; D003201:Computers; D015195:Drug Design; D000939:Epitopes / Q000737:chemistry; D018984:Epitopes, T-Lymphocyte / Q000737:chemistry; D015658:HIV Infections / Q000517:prevention & control* / Q000821:virology; D015497:HIV-1 / Q000235:genetics* / Q000276:immunology*; D006801:Humans; D020407:Internet; D012984:Software; D013601:T-Lymphocytes / Q000378:metabolism*; D013678:Technology, Pharmaceutical / Q000295:instrumentation*; D014612:Vaccines / Q000737:chemistry*
D016915:AIDS Vaccines; D000941:Antigens; D000939:Epitopes; D018984:Epitopes, T-Lymphocyte; D014612:Vaccines