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Welcome to Vaxign: Vaccine Design!

Vaxign2 is now available! Click here to try it out.

Vaxign (Vaccine Design) is a vaccine target prediction and analysis system based on the principle of reverse vaccinology. Two programs exist in Vaxign: (1) Vaxign Query: provide precomputed Vaxign results for users to explore, and (2) Dynamic Vaxign Analysis: allow sequence input and dynamic Vaxign execution and result visualization.

NOTE: Vaxign is freely available for academic uses. The Vaxign vaccine design pipeline runs some open-access third-party software programs/algorithms in the background. For commercial users, you may want to check all licenses for these third-party programs used in Vaxign.

1. Vaxign Query:

     This program allows users to search precomputed Vaxign results for > 350 genomes. A user can either select a genome(s) for all possible vaccine targets based on desired parameters, or query a protein sequence(s) from a genome to find possible vaccine vaccine target(s):

Select a Genome(s), Query a Protein (Optional), and Set up Parameters (Optional)
Select a Genome Group (Required)
Select a Genome (Required)
Sequence ID(s) (One ID per line, or use comma, tab-delimited format)
Or load IDs from file
Sort by
Filter Options:
1. Select Subcellular Localization
2. Number of Transmembrane Helices (Note: check to include this filtering option)
3. Adhesin Probability (0-1.0) (Note: check to include this filtering option)
4. Have Orthologs in
of the above selected genomes
5.Exclude Proteins having Orthologs
in Any of Selected Genome(s)

6. Similarity to Host Proteins
7. Similarity to Mouse Proteins
8. Similarity to Pig Proteins
9. MHC class I and II epitope prediction Note: This function is available after initial protein filtering

To select (or unselect) individual genomes, press Ctrl key and then select; For genome selection in continuous order, you can also use Shift key.

2. Dynamic Vaxign Analysis:

     This program allows users to input a protein sequence(s) and set up parameters. The Vaxign web server will dynamically calculate the possibilities of using the protein(s) as vaccine target(s) using the automatic Vaxign pipeline. It is noted that lengthy computational time may be expected.

Input Protein Sequence(s), Set up Parameters, and Submit a Job
Protein Sequence(s):
(Examples: Gram- B. abortus SodC, Gram+ Bacillus anthracis PA, 62317454, or YP_016495.2)
(Note: Select FASTA or other format, up to 500 sequences)
Sequence Format
File Upload
Bacterium Gram -/+ (NOT for Virus)
Include Analyses [Select all] [Unselect all]
  • Subcellular Localization
  • Transmembrane Helices
  • Adhesion Probability
  • MHC Class I Binding
  • MHC Class II Binding
  • Similarity to Host Proteins Human Mouse Pig
Your Note:

Link To: Please cite the following Vaxign references:

  1. He Y, Xiang Z, Mobley HLT. Vaxign: the first web-based vaccine design program for reverse vaccinology and an application for vaccine development.J Biomed Biotechnol. 2010;2010:297505. Epub 2010 Jul [PMID:20671958] [Journal Link]
  2. Xiang Z, He Y. 2009. Vaxign: a web-based vaccine target design program for reverse vaccinology. Procedia in Vaccinology. Volume 1, Issue 1, Pages 23-29.      
  3. Xiang Z, He Y. Genome-wide prediction of vaccine targets for human herpes simplex viruses using Vaxign reverse vaccinology. BMC Bioinformatics. 2013, 14(Suppl 4):S2 (8 March 2013). PMID: 23514126; PMCID: PMC3599071.

Please see the Vaxign Documentation for more information.

Please contact us if you would like to have your favorite genome(s) included in our precomputed Vaxign database. Your suggestions and comments are welcome. Thank you.