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Welcome to Vaxign2: Vaccine Design!

Vaxign2 (Vaccine Design) is a vaccine target prediction and analysis system based on the principle of reverse vaccinology.
Two methods in Vaxign2 are:
     (1) Dynamic Analysis: allow sequence input and dynamic Vaxign2 execution and result visualization.
     (2) Precompute Query: provide precomputed Vaxign2 results for users to explore

This program allows users to input a protein sequence(s) and set up parameters. The Vaxign2 web server will dynamically calculate the possibilities of using the protein(s) as vaccine target(s) using the automatic Vaxign2 pipeline. It is noted that lengthy computational time may be expected.

Input Protein Sequence(s)
Protein Sequence(s):
(Examples: Gram- B. abortus SodC, Gram+ Bacillus anthracis PA, 62317454, or YP_016495.2)
Sequence Format
File Upload
Set up Parameters
Vaxign2 uses multiple open-source software programs and databases for analysis.

For more information on these programs and their licenses, please click here to view the Vaxign2 docs.
Select Pathogen Organism Type:
Include Basic Vaxign Analyses: [Default] [Select all] [Unselect all]
Include Vaxign-ML Analysis?
Vaxign-ML is a machine learning-based reverse vaccinology prediction program.

For detail about Vaxign-ML, please click here.
Include Vaxitop Analysis?
Vaxign-ML is the an MHC Class I and II binding epitope prediction program.

For detail about Vaxitop, please click here.
Submit a Job 
Submission Note:
Notify via Email:
help

Query from > 350 genomes precomputed Vaxign2 results.

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 (Required)
Click here for tutorial
Select a Genome Group (Required)
Select a Genome (Required)
Choose a Protein (Optional)
Sequence ID(s) (One ID per line, or use comma, tab-delimited format)
Or load IDs from file
Keywords
Set up Filter (Optional) hide
Vaxign2 uses multiple open-source software programs and databases for analysis.

For more information on these programs and their licenses, please click here to view the Vaxign2 docs.
1. Select Subcellular Localization (PSORTb)
2. Number of Transmembrane Helices (TMHMM) (Check to include this filter)
3. Adhesin Probability (0-1.0) (SPAAN) (Check to include this filte)
4. Have Orthologs in 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.

selected 0 genomes
5.Exclude Proteins having Orthologs
in Any of Selected Genome(s) 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.

selected 0 genomes
6. Similarity to Human Proteins (BLAST)
7. Similarity to Mouse Proteins (BLAST)
8. Similarity to Pig Proteins (BLAST)
help

Link To: Citing Vaxign2:
Edison Og, Michael F Cooke, Anthony Huffman, Zuoshuang Xiang, Mei U Wong, Haihe Wang, Meenakshi Seetharaman, Ninotchka Valdez, Yongqun He, Vaxign2: the second generation of the first Web-based vaccine design program using reverse vaccinology and machine learning, Nucleic Acids Research, 2021 [Journal Link]

Link To: Citing the original Vaxign proceeding:
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.      

Link To: Related Vaxign Publications:
1. 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.