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Vaxign specifications


Unique identifier OMICS_20486
Name Vaxign
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input data Amino acid sequences from one protein or whole genomes, NCBI protein GI, or RefSeq accession number
Input format FASTA
Output format web link
Computer skills Basic
Stability Stable
Registration required Yes
Maintained Yes



  • person_outline Yongqun He <>

Additional information

Vaxign is part of VIOLIN

Publication for Vaxign

Vaxign citations


In silico Design, and In vitro Expression of a Fusion Protein Encoding Brucella abortus L7/L12 and SOmp2b Antigens

PMCID: 5840964
PMID: 29531919
DOI: 10.4103/abr.abr_10_17

[…] abortus vaccine strain 19, studied by bioinformatics analysis of the strain, indicates that omp2b probably contributes to the attenuation of this mutant. additionally, analysis of brucella genome by vaxign demonstrated that omp2b is present in b. abortus, b. melitensis, b. suis and b. canis strains that are pathogenic to humans, but absent from brucella ovis that is nonpathogenic to humans.[] […]


Promising new vaccine candidates against Campylobacter in broilers

PMCID: 5703506
PMID: 29176789
DOI: 10.1371/journal.pone.0188472

[…] (mccda) for 48 h or in brucella broth for 24 h., from c. jejuni 81–176 genomic dna, genes encoding yp_001000437.1, yp_001000562.1, yp_001001115.1, yp_999769.1, yp_999817.1, and yp_999838.1 from the vaxign database (named yp437, yp562, yp1115, yp9769, yp9817, and yp9838 hereinafter) were amplified by polymerase chain reaction (pcr) (primers listed in ), using the vent® dna polymerase (neb) […]


Identification of New Features from Known Bacterial Protective Vaccine Antigens Enhances Rational Vaccine Design

PMCID: 5662880
PMID: 29123525
DOI: 10.3389/fimmu.2017.01382

[…] (ap) has not been widely appreciated. other criteria including signal peptides, conserved domains, and biological function analysis () have been used in different rv tools [e.g., nerve (), vaxign (), and jenner-predict server ()], and machine-learning techniques are also applied to vaccine design studies (, ). however, the significance and association of above criteria […]


Immunoprotective potential of BamA, the outer membrane protein assembly factor, against MDR Acinetobacter baumannii

PMCID: 5622086
PMID: 28963492
DOI: 10.1038/s41598-017-12789-3

[…] against bacterial challenge–,,. in this work, we showed that bama is highly conserved in a. baumannii and has the ability to evoke immune response in mice leading to efficient immunoprotection., vaxign predicted bama a potential vaccine candidate as it is an outer membrane protein as predicted by psortb (p > 0.9) with high adhesion probability, no trans-membrane helices and complete […]


Computational Identification and Characterization of a Promiscuous T Cell Epitope on the Extracellular Protein 85B of Mycobacterium spp. for Peptide Based Subunit Vaccine Design

PMCID: 5376426
PMID: 28401156
DOI: 10.1155/2017/4826030

[…] (tb) is a reemerging disease that remains as a leading cause of morbidity and mortality in humans. to identify and characterize a t-cell epitope suitable for vaccine design, we have utilized the vaxign server to assess all antigenic proteins of mycobacterium spp. recorded to date in the protegen database. we found that the extracellular protein 85b displayed the most robust antigenicity […]


Ontology based literature mining of E. coli vaccine associated gene interaction networks

PMCID: 5348867
PMID: 28288685
DOI: 10.1186/s13326-017-0122-4

[…] coli gene name normalization. to integrate e. coli gene names from different e. coli genome annotations, we applied the pan-genome strategy [, ]. specifically, out of 75 e. coli strains, we used the vaxign program [], which includes the orthomcl ortholog searching program [], to generate an e. coli pan-genome that includes core e. coli genes shared by all strains, and dispensable genes present […]

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Vaxign institution(s)
Unit for Laboratory Animal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA; Center for Computational Medicine and Biology, University of Michigan Medical School, Ann Arbor, MI, USA
Vaxign funding source(s)
Supported by the Center for Computational Medicine and Bioinformatics (CCMB) at the University of Michigan Medical School, MI, USA; Public Health Service grants AI43363 and AI081062 from the National Institutes of Health.

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