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Welcome to Vaxign: Vaccine Design!

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

Note: Sorry that Vaxign and Vaxign2 both have some bug(s) that we are still fixing. Before it is fixed, please download and use the Vaxign-ML-docker for your prediction.

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)	Please select a genome group Acinetobacter baumannii (35) Aeromonas hydrophila (2) African swine fever virus (3) Bacillus anthracis (3) Brucella (31) Campylobacter (10) Clostridium (10) Clostridium difficile (13) Coronavirus (8) Corynebacterium (14) Coxiella burnetii (5) Escherichia coli (11) Flavobacterium columnare (1) Francisella (9) Haemophilus influenzae (4) Helicobacter pylori (6) Herpesvirus (52) Human immunodeficiency virus (2) Legionella pneumophila (9) Listeria monocytogenes (3) Lymphocystis virus (4) Measles virus (1) Mycobacterium (15) Mycoplasma bovis (2) Mycoplasma hyopneumoniae (3) Mycoplasma mycoides (4) Neisseria meningitidis (4) Rickettsia (1) Salmonella (23) Shigella (5) Staphylococcus aureus (33) Streptococcus (53) Streptococcus pneumoniae (1) Vaccinia virus (1) Variola virus (1) Vibrio (22) Yellow fever virus (1)
Select a Genome (Required)	Please select a genome
Sequence ID(s)	NCBI Protein Accession NCBI Protein GI NCBI Gene ID Locus Tag (One ID per line, or use comma, tab-delimited format) Or load IDs from file
Keywords	Gene Symbol Protein Note
Sort by	NCBI Protein RefSeq NCBI Protein GI Gene Symbol Loalization Loalization Probability Adhesin Probability Protein Note Ascending Descending
Filter Options:
1. Select Subcellular Localization	Any Localization Cellwall Cytoplasmic Cytoplasmic Membrane Extracellular Outer Membrane Periplasmic Unknown
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	Yes No Do not use this option
7. Similarity to Mouse Proteins	Yes No Do not use this option
8. Similarity to Pig Proteins	Yes No Do not use this option
9. MHC class I and II epitope prediction	Note: This function is available after initial protein filtering
help

     Tips: 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 Protein Sequence (Fasta Format) Protein GI Protein RefSeq Accession Gene ID Gene Locus Tag Protein Sequence (Fasta file links)

File Upload

Bacterium Gram -/+ (NOT for Virus) Gram negative bacterium Gram positive bacterium Archaea

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:

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.