Vaxign: The First Web-Based Vaccine Design Program for Reverse Vaccinology and Applications for Vaccine Development

TLDR

Vaxign is the first web‑based reverse vaccinology platform that predicts vaccine targets from genome sequences. The authors used Vaxign to predict UPEC vaccine candidates and compared them with experimental data to demonstrate the program’s utility. Vaxign predicts targets by evaluating subcellular location, transmembrane helices, adhesin probability, conservation, exclusion of nonpathogenic genomes, and MHC class I/II epitope binding, and it offers a precomputed database for over 70 genomes plus dynamic prediction for user‑supplied sequences. The results show that Vaxign is accurate and efficient for vaccine design.

Abstract

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<mml:math xmlns:mml="http://www.w3.org/1998/Math/MathML"><mml:mo>&gt;</mml:mo><mml:mn>70</mml:mn></mml:math>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.