Vaxign: a web-based vaccine target design program for reverse vaccinology

In the post-genomic era, strategies of vaccine development have progressed dramatically from traditional Pasteur's principles of isolating, inactivating and injecting the causative agent of an infectious disease, to reverse vaccinology that starts from bioinformatics analysis of the genome information. Based on the reverse vaccinology strategy, we have developed a web-based vaccine design system called Vaxign (http://www.violinet.org/vaxign/). Vaxign predicts possible vaccine targets based on various vaccine design criteria using microbial genomic and protein sequences as input data. Major predicted features in the Vaxign pipeline include subcellular location of a protein, transmembrane domain, adhesion probability, sequence conservation among genomes, sequence similarity to host (human or mouse) proteome, and epitope binding to MHC class I and class II. This pipeline integrates both existing open source tools and internally developed programs with user-friendly web interfaces. A user can either query pre-computed Vaxign results for one protein sequence(s) from one genome(s) or perform dynamic analysis on input protein sequence(s). Vaxign has stored pre-computed results from more than 40 genomes from various pathogens (e.g., Brucella). The analysis results indicate that Vaxign specifically and sensitively predicts known vaccine targets and also provides new vaccine target candidates. Vaxign is part of the web-based system called Vaccine Investigation and Online Information Network (VIOLIN, http://www.violinet.org). Vaxign is a freely available program that facilitates vaccine researchers to efficiently design vaccine targets and develop vaccines using rationale reverse vaccinology.