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Two Methods

Vaxign Query

Dynamic Analysis

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Welcome to Vaxign: Vaccine Design!

     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 the public to use, including commercial usage. For commercial users, you may want to check all licenses for those third-party programs used in Vaxign.

1. Vaxign Query:

     This program allows users to search precomputed Vaxign results for > 100 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 (Required)	Please select a genome Bacillus anthracis str. 'Ames Ancestor' Bacillus anthracis str. Ames Bacillus anthracis str. Sterne Brucella abortus 2308 Brucella abortus biovar 1 str. 9-941 Brucella abortus bv. 2 str. 86/8/59 Brucella abortus bv. 3 str. Tulya Brucella abortus bv. 4 str. 292 Brucella abortus bv. 6 str. 870 Brucella abortus bv. 9 str. C68 Brucella abortus NCTC 8038 Brucella abortus S19 Brucella canis ATCC 23365 Brucella ceti B1/94 Brucella ceti M13/05/1 Brucella ceti M490/95/1 Brucella ceti M644/93/1 Brucella melitensis 16M Brucella melitensis ATCC 23457 Brucella melitensis bv. 1 str. Rev.1 Brucella melitensis bv. 2 str. 63/9 Brucella melitensis bv. 3 str. Ether Brucella microti CCM 4915 Brucella neotomae 5K33 Brucella ovis ATCC 25840 Brucella pinnipedialis B2/94 Brucella pinnipedialis M163/99/10 Brucella pinnipedialis M292/94/1 Brucella sp. F5/99 Brucella suis 1330 Brucella suis ATCC 23445 Brucella suis bv. 3 str. 686 Brucella suis bv. 4 str. 40 Brucella suis bv. 5 str. 513 Campylobacter concisus 13826 Campylobacter curvus 525.92 Campylobacter fetus subsp. fetus 82-40 Campylobacter hominis ATCC BAA-381 Campylobacter jejuni RM1221 Campylobacter jejuni subsp. doylei 269.97 Campylobacter jejuni subsp. jejuni 81-176 Campylobacter jejuni subsp. jejuni 81116 Campylobacter jejuni subsp. jejuni NCTC 11168 Campylobacter lari RM2100 Clostridium botulinum A str. ATCC 19397 Clostridium botulinum A str. ATCC 3502 Clostridium botulinum A str. Hall Clostridium botulinum A2 str. Kyoto str. Kyoto-F Clostridium botulinum A3 str. Loch Maree Clostridium botulinum B str. Eklund 17B Clostridium botulinum B1 str. Okra okra Clostridium botulinum E3 str. Alaska E43 Clostridium botulinum F str. Langeland Clostridium tetani E88 Corynebacterium diphtheriae NCTC 13129 Coxiella burnetii CbuG_Q212 Coxiella burnetii CbuK_Q154 Coxiella burnetii Dugway 5J108-111 Coxiella burnetii RSA 331 Coxiella burnetii RSA 493 Escherichia coli 536 Escherichia coli CFT073 Escherichia coli F11 Escherichia coli O157:H7 EDL933 Escherichia coli O157:H7 str. Sakai Escherichia coli str. K-12 substr. MG1655 Escherichia coli UTI89 Francisella philomiragia subsp. philomiragia ATCC 25017 Francisella tularensis subsp. holarctica Francisella tularensis subsp. holarctica FTNF002-00 Francisella tularensis subsp. holarctica OSU18 Francisella tularensis subsp. mediasiatica FSC147 Francisella tularensis subsp. novicida U112 Francisella tularensis subsp. tularensis FSC198 Francisella tularensis subsp. tularensis SCHU S4 Francisella tularensis subsp. tularensis WY96-3418 Haemophilus influenzae 86-028NP Haemophilus influenzae PittEE Haemophilus influenzae PittGG Haemophilus influenzae Rd KW20 Helicobacter pylori 26695 Helicobacter pylori G27 Helicobacter pylori HPAG1 Helicobacter pylori J99 Helicobacter pylori P12 Helicobacter pylori Shi470 Human immunodeficiency virus 1 Human immunodeficiency virus 2 Legionella pneumophila str. Corby Legionella pneumophila str. Lens Legionella pneumophila str. Paris Legionella pneumophila subsp. pneumophila str. Philadelphia 1 Listeria monocytogenes EGD-e Listeria monocytogenes HCC23 Listeria monocytogenes str. 4b F2365 Measles virus Mycobacterium tuberculosis CDC1551 Mycobacterium tuberculosis H37Rv Neisseria meningitidis 053442 Neisseria meningitidis FAM18 Neisseria meningitidis MC58 Neisseria meningitidis Z2491 NERVE gram negative NERVE gram postive Rickettsia prowazekii str. Madrid E Shigella boydii CDC 3083-94 BS512 Shigella boydii Sb227 Shigella dysenteriae Sd197 Shigella flexneri 2a str. 2457T Shigella flexneri 5 str. 8401 Vaccinia virus Variola virus Vibrio cholerae M66-2 Vibrio cholerae O1 biovar eltor str. N16961 Vibrio cholerae O395 Yellow fever virus
Keywords	Locus Tag Gene Symbol NCBI GeneID NCBI Protein RefSeq NCBI Protein GI Protein Description
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. Maximum Number of Transmembrane Helices	(Note: check box to include)
3. Minimum Adhesin Probability (0-1.0)
4. Have Orthologs in	of the above selected genomes
5.Exclude Proteins having Orthologs in Any of Selected Genome(s)
6. No Similarity to Human Proteins
7. No Similarity to Mouse Proteins
8. MHC Class I & II Epitope Prediction by Vaxitope:
P Value Cutoff
MHC Host Species	any species human mouse chimpanzee macaque
MHC Allele	any allele
Epitope Length	any length
help

     Tips: To select (or unslect) 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 a Protein Sequence(s), Set up Parameters, and Submit a Job

Protein Sequence(s) (FASTA format, NCBI proten GI or RefSeq Accession Number) (Examples: Gram- B. abortus SodC, Gram+ Bacillus anthracis PA, 62317454, or YP_016495.2) (Note: Up to 300 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) negative positive

Include Analyses [Select all] [Unselect all] Subcellular Localization Transmembrane Helices Adhesion Probability MHC Class I Binding MHC Class II Binding Similarity to Human Proteins Similarity to Mouse Proteins

Please see the Vaxign Documentation . 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.