Vaxign: the first web-based vaccine design program for reverse vaccinology and applications for vaccine development

J Biomed Biotechnol. 2010:2010:297505. doi: 10.1155/2010/297505. Epub 2010 Jul 4.


Vaxign is the first web-based vaccine design system that predicts vaccine targets based on genome sequences using the strategy of reverse vaccinology. Predicted features in the Vaxign pipeline include protein subcellular location, transmembrane helices, adhesin probability, conservation to human and/or mouse proteins, sequence exclusion from genome(s) of nonpathogenic strain(s), and epitope binding to MHC class I and class II. The precomputed Vaxign database contains prediction of vaccine targets for >70 genomes. Vaxign also performs dynamic vaccine target prediction based on input sequences. To demonstrate the utility of this program, the vaccine candidates against uropathogenic Escherichia coli (UPEC) were predicted using Vaxign and compared with various experimental studies. Our results indicate that Vaxign is an accurate and efficient vaccine design program.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms
  • Bacterial Outer Membrane Proteins / immunology
  • Biotechnology / methods*
  • Epitopes / immunology
  • Genome, Bacterial / genetics
  • Histocompatibility Antigens Class I / immunology
  • Internet*
  • ROC Curve
  • Reproducibility of Results
  • Sequence Analysis, DNA
  • Software*
  • Uropathogenic Escherichia coli / genetics
  • Uropathogenic Escherichia coli / immunology
  • User-Computer Interface
  • Vaccines / chemical synthesis*
  • Vaccines / immunology


  • Bacterial Outer Membrane Proteins
  • Epitopes
  • Histocompatibility Antigens Class I
  • Vaccines