VBASE3 Official Logo
VBASE3 Beta β€’ DNAPLOT
Comparative Immunogenomics & Synthesis Database
πŸ“’ Beta Release Community Feedback Welcome
πŸ›οΈ Systematic Tripartite Repertoires (V, D, J) β€’ ⚑ 100% Client-Side WebAssembly β€’ πŸ›‘οΈ Class I Confirmed Functional Only β€’ πŸ“œ Zenodo Release (DOI: 10.5281/zenodo.22923345)

Comparative Immunogenomics Across Jawed Vertebrates

VBASE3 provides an independent, open, and synthesis-ready tripartite antibody and TCR gene database containing 2,857 canonical Class I genes in the master export (2,651 V, 93 D, and 113 J segments) spanning 53 vertebrate species taxa, alongside 8,329 total functional alleles across 43 species-level catalogs, 3,114 curated TCRBase genes, 2,048 PaCMAP manifold points, and 3,900 Rosetta Stone cross-database mappings. Screened across 55 chromosome-level reference assemblies and verified against over 46 million physiological repertoire reads with sub-millisecond Rust SIMD vector alignment and strict IMGT synthesis boundaries (TVSS/TVSA for Heavy; VEIK/LEIK for Kappa; TVL for Lambda), every sequence is classified based on empirical physiological rearranged evidence with zero constant region bleed-through.

⚑ Launch DNAPLOT Analysis Studio → 🌌 PaCMAP Universe (2,048 Points) → πŸ“Š Assembly Status & Coverage → πŸ“ˆ Single-Cell Paired Studio →
2,857
Class I Master Export
2,651 V β€’ 93 D β€’ 113 J Curated
8,329
Total Functional Alleles
Across 43 Species-Level Catalogs
2,048
Live PaCMAP Manifold Points
2D Pan-Vertebrate V-Gene Map
3,114
TCRBase Genes in VBASE3
TRA / TRB / TRG / TRD across 31 spp.
53
Species Taxa in Master Release
Screened across 55 Assemblies
3,900
Rosetta Stone Mappings
Cross-Database Universal IDs
πŸ“₯
Universal Sequence Dropzone & Smart Router
Drop any antibody or TCR sequence file (.fasta, .fa, .tsv, .csv, .txt) or paste sequence below. The client-side engine automatically deduces receptor (BCR vs TCR), species, and locus, and routes directly into the ideal analyzer.
🧭 Guided Pathways: Which VBASE3 Mode Fits Your Goal?
Dedicated application pathways for evolutionary biologists, software tool developers, biologics engineers, onco-immunologists, and curious learners
🧬
Evolutionary Explorer
Phylogeny & Framework Clans

Interrogate 500 million years of vertebrate immunity. Test conservation of Dildrop Clans I–III, structural convergence in shark VNAR vs. camelid VHH, allotetraploid Xenopus subgenome divergence, and light-chain isotype shifts.

✦ Vertebrate PaCMAP Universe (2,048 points, 32 spp.)
✦ TCRBase Master Repertoire across 31 species
✦ Bovine Ultralong Stalk-Knob Loops (up to 68 aa)
✦ Xenopus Long vs. Short Subgenomes
🌌 Open PaCMAP Universe →
Pan-Vertebrate Xenopus Subgenomes
πŸ’»
Bioinformatician & AI
Data Ingestion & Pipelines

Enhance software and train models with 100% Class I confirmed functional germline catalogs. Train protein language models (ESM-2) and structural predictors (AlphaFold, IgFold) with canonical boundaries.

✦ Master Class I Catalogs (2,857 genes, 53 spp.)
✦ Rosetta Stone Cross-Reference (DP, VBASE2, IMGT)
✦ Headless WebAssembly CLI via Node.js
✦ Model Context Protocol (MCP) Server for AI
πŸ›οΈ Open Rosetta Stone →
Status & Coverage GitHub Data & MCP β†—
πŸ”¬
Biologics Engineer
Therapeutic Design & Synthesis

Rational design of mAbs, nanobodies (VHH), and bispecifics. Screen developability liabilities (NG/DG, free cysteines, glycosylation), optimize pairing, and enforce strict synthesis boundaries (TVSS/VEIK/TVL).

✦ Developability Liability Audits (NG, DG, Cys)
✦ Nanobody FR2 Solubility Verification
✦ Bispecific Cognate Pairing Fidelity
✦ 1-Click Vendor Order Sheets (TVSS/VEIK/TVL)
⚑ Launch Human Biologics Suite →
VHH Nanobody Rabbit / Dog
🩺
Onco-Immunology
Lymphoma Clonality & Repertoire Dynamics

Monitor immune interventions and detect malignant clonal expansions. Track longitudinal vaccination/infection kinetics, identify lymphoma/leukemia spikes (DLBCL, FL, CLL, CTCL), evaluate ongoing SHM subclonal trees, and monitor MRD down to 10⁻⁢.

✦ Lymphoma / Leukemia Monoclonal Spikes
✦ Longitudinal SHM Velocity & Kinetics Curves
✦ Ongoing SHM & Subclone Evolution Trees
✦ CLL Stereotyped BCR Subsets & MRD Tracking
πŸ“ˆ Open Single-Cell Repertoire Studio →
DNAPLOT Subclones Time-Series Kinetics
πŸŽ“
Curious Explorer
The VBASE2 Legacy & Fun Learning

New to antibody genomics? No prior sequence needed! Click 1-click landmark presets to explore famous therapeutics (Herceptin) and classic hybridomas (B1-8). Learn through interactive 2D pearl necklaces with zero fear.

✦ 1-Click Landmark Presets on every page
✦ Interactive Collier de Perles 2D pearl necklace
✦ Forgiving Sequence Intake & plain explanations
✦ Playful Discovery without intimidating errors
✨ Try DNAPLOT with Presets →
Murine B1-8 Preset Nanobody Preset
πŸ”¬ Flagship Species WebAssembly Analyzers & DNAPLOT Suite
Dedicated client-side V(D)J alignment, single-cell paired VH:VL matrix mining, and CDR3 extraction
⚑
DNAPLOT Analysis Studio
Universal V(D)J Alignment & Junction Analysis
Flagship sequence alignment & deconstruction suite. Performs real-time germline V(D)J matching, junction deconstruction (V, P, N1, D, N2, J), somatic hypermutation tracking, and interactive IMGT Collier de Perles 2D pearl necklaces.
⚑ Rust SIMD128 Collier de Perles Junction Deconstruction All Species
⚑ Launch DNAPLOT Studio →
πŸ‘€
Human VBASE3 Portal
Homo sapiens β€’ Tripartite Suite
2,106 mature V-genes, 32 D-segments, 28 J-segments. Includes Single-Cell Paired VH:VL Matrix, CDR3 length distribution, and Bulk Repertoire Profiler.
Heavy (IGH) Kappa (IGK) Lambda (IGL) Paired Single-Cell
⚑ Launch Human Analyzer →
🐭
Mouse VBASE3 Portal
Mus musculus β€’ Dildrop & Hybridomas
2,763 functional germlines across 14 Renate Dildrop families (J558, 7183, Q52, S107). Landmark hybridoma controls (B1-8, 17.2.25 QM, OKT3) and kappa-dominant analysis.
14 VH Families Hybridomas Tomlinson Mappings
⚑ Launch Mouse Analyzer →
πŸ¦™
Camelid VHH / Nanobody
Alpaca & Llama β€’ Heavy-Chain-Only
Heavy-chain-only antibodies (VHH). Automatic detection of hallmark FR2 hydrophobic substitutions (F/Y37, E44, R45, G47) and extended disulfide loops.
VHH Nanobodies FR2 Hallmarks Long CDR3
⚑ Launch Camelid Portal →
πŸ‡
Rabbit RabMAb Analyzer
Oryctolagus cuniculus β€’ High-Affinity
Repertoire analyzer for rabbit monoclonal antibodies. Tracks dominant VHa1/VHa2 lineages and detects canonical inter-CDR extra disulfide bridges (Cys80–Cys171).
RabMAb Extra Cysteines VHa Lineages
⚑ Launch Rabbit Analyzer →
πŸ•
Dog / Canine Vet-mAb
Canis lupus familiaris β€’ Veterinary
Canine immunoglobulin repertoire workbench for veterinary biologics discovery, caninization engineering, and kappa/lambda isotype profiling.
Canine mAb Veterinary Biologics Caninization
⚑ Launch Dog Analyzer →
πŸ”
Chicken / Avian IgY
Gallus gallus β€’ Gene Conversion
Avian antibody repertoire utilizing single functional V-gene loci with somatic gene conversion from upstream pseudo-V donor arrays.
Avian IgY Gene Conversion Pseudo-V Arrays
⚑ Launch Chicken Analyzer →
🐸
Xenopus Amphibian Portal
Du Pasquier & Hsu β€’ Tetrapod Evolution
Historical ectothermic immunogenetics from Louis Du Pasquier & Ellen Hsu. Explores ancient amphibian IgM, IgX, IgY, and light-chain isotypes (Rho & Sigma).
Amphibians IgM / IgX / IgY Igρ & IgΟƒ Light
⚑ Launch Xenopus Portal →
Archival Data Release Permanent Open Science Repository & Master Catalogs

Download VBASE3 Master Datasets, FASTA Libraries & Publication Manuscript

All 2,857 Class I confirmed functional genes across 36 benchmark taxa, 3,114 curated TCRBase germlines, 3,900 Rosetta Stone cross-mappings, modular Fc constant cassettes with GenBank provenance, and the full peer-reviewed monograph are permanently archived on Zenodo (DOI: 10.5281/zenodo.22923345).

πŸ“¦ Download from Zenodo β†—
πŸ›οΈ Comparative Reference Databases & Universes
Multi-species constant regions, PaCMAP manifolds, TCR repertoires, and coverage benchmarks
πŸ›οΈ
Constant Regions Database
CH1-3, CL, Hinge, Allotypes & Synthesis
Independent catalogue of verified constant region exons across mammalian & non-mammalian isotypes (IgG1-4, IgM, IgA, IgE, IgD, IgY, IgW, IgNAR) with 1-click synthesis exports.
Fc Engineering Hinge Motifs GenBank Linked
⚑ Open Constant Regions →
🌌
PaCMAP V-Gene Universe
2D Dimensionality Reduction (2,048 Points)
Interactive structural manifold embedding 2,048 Class I confirmed functional V-genes across 32 comparative vertebrate taxa with real-time zero-shift projection.
32 Taxa 2,048 Points PaCMAP 2D BCRbase
⚑ Explore PaCMAP Universe →
🧬
TCRBase TCR Universe
Ξ±Ξ² & Ξ³Ξ΄ T-Cell Receptors across 31 Species
Vertebrate T-Cell Receptor Universe (3,114 Genes, 9 D-Genes, 91 J-Genes). Systematic Clan & Orthogroup nomenclature across human, mouse, and vertebrates.
TRA & TRB TRG & TRD Systematic Clans
⚑ Launch TCRbase Universe →
πŸ‘€
Human TCR Analyzer
Homo sapiens TRA, TRB, TRG, TRD Domain Suite
Dedicated human T-cell receptor analyzer (283 V-genes, 5 D-genes, 75 J-genes). Pre-loaded viral (EBV, CMV), tumor neoantigen (1G4 NY-ESO-1), MAIT, and Ξ³Ξ΄ benchmarks with live 2D PaCMAP projection.
283 Human TCRs 12/23 RSS Diode Tumor TILs
⚑ Launch Human TCR Analyzer →
🐁
Mouse TCR Analyzer
Mus musculus TRA, TRB, TRG, TRD Domain Suite
Dedicated murine T-cell receptor analyzer (290 V-genes, 4 D-genes, 16 J-genes). Pre-loaded OT-I, OT-II, P14, 2B4, and epidermal DETC invariant Ξ³Ξ΄ benchmarks with live 2D PaCMAP projection.
290 Mouse TCRs OT-I / OT-II DETC Ξ³Ξ΄
⚑ Launch Mouse TCR Analyzer →
⚑
DNAPLOT SIMD Engine
Rust SIMD128 Sequence Alignment
Canonical high-speed V(D)J alignment, junction deconstruction, and somatic hypermutation analysis suite with IMGT Collier de Perles coordinate generation.
Rust SIMD Collier de Perles DNAPLOT Reports
⚑ Launch DNAPLOT Studio →
πŸ“Š
Expressed Repertoire Diversity
AIRR Manifold & Frequency Analytics
Multi-dataset manifold containing complete V(D)J sequences, hypervariable CDR3 loops, and paired single-cell BCRs across viral infection and baseline cohorts.
AIRR Datasets CDR3 Spectra 46M+ Sequences
⚑ View Repertoire Diversity →
πŸ”¬
Single-Cell Repertoire Studio
Paired VH:VL Analytics & GxP Provenance
High-throughput single-cell paired antibody analyzer. Interactive VH Γ— VL combinatorial matrix, clonal expansion trees, and synthesis-ready order sheets with ISO audit metadata.
Paired Single-Cell Audit Provenance Order Sheets
⚑ Launch Single-Cell Studio →
πŸ“ˆ
Status & Coverage Monitor
Objective 80% Coverage Gating Policy
Quality gating and assembly monitoring. Tracks live portals vs. maturing draft assemblies, invariant validation checks, and locus completeness.
Gating Policy Assembly Tracking Quality Metrics
⚑ Check Species Coverage →
⚑ In-Browser Exploration Sandbox
Query GenBank frequencies, inspect IMGT gapped germlines, and run instant DNAPLOT WASM analysis inline
🐭 Mouse Heavy Chain (musIGHV) Top V-Gene Frequencies
Rank V-Gene Symbol IMGT Allele GenBank Frequency Classic Name / Family Biological Milestone
Data Source: GenBank Expressed Physiological Repertoires (Benson et al., 2013) β†— VBASE3 Last Updated: September 16, 2026
Species:
Chain:
πŸ”₯ Top CDR3 Clonal Expansions
Rank CDR3 Amino Acid Sequence Sequence Count Frequency %
Click options above to load data.
Data Source: AIRR Community Physiological Clonal Expansions (Breden et al., 2017; Vander Heiden et al., 2018) β†— VBASE3 Last Updated: September 16, 2026
⚑ Looking for the complete DNAPLOT Analysis Studio?
Includes full IMGT Collier de Perles 2D pearl necklaces, junction deconstruction (V/D/J/N1/N2), 1-128 coordinate grids, and landmark clinical controls.
πŸš€ Open Full DNAPLOT Studio (dnaplot.html) →
Load Landmark Sample:
πŸ’» Command Line & Node.js WASM Execution
Node.js v18+ Compatible

The exact same client-side WebAssembly binary (dnaplot_wasm_bg.wasm) can be invoked directly from the terminal or integrated into high-throughput Node.js pipelines without a browser:

# 1. Run canonical landmark sample from terminal:
node developer_scripts/vbase3_wasm_cli.mjs --sample humIGHV3-23

# 2. Analyze query sequence with custom species hint:
node developer_scripts/vbase3_wasm_cli.mjs --seq "CAGGTACAGCTGAAGGAGTC..." --species mouse

# 3. Batch repertoire processing with AIRR TSV output:
node developer_scripts/vbase3_wasm_cli.mjs --fasta sample.fasta --format tsv
CLI Runner: developer_scripts/vbase3_wasm_cli.mjs VBASE3 Last Updated: September 16, 2026
Select a tool above to run analysis.
πŸ“š Key Scientific Literature & References
Direct links to peer-reviewed foundational literature, sequence directories, nomenclature authorities, and empirical dataset citations
VBASE3 Flagship Release
VBASE3: An Open Immunogenomics Database and Alignment Engine for Jawed Vertebrates
Mueller, W. (2026)
Zenodo Open Science Archive & Comparative Immunogenomics Monograph
πŸ“„ DOI: 10.5281/zenodo.22923345 β†— πŸ’» GitHub Repository β†—
VBASE2 Relational Database
VBASE2, an integrative V gene database
Retter, I., Althaus, H.-H., MΓΌnch, R., & MΓΌller, W. (2005)
Nucleic Acids Research, 33(Database Issue), D671–D674
πŸ“„ DOI: 10.1093/nar/gki088 β†— πŸ”¬ PubMed: 15608286 β†— πŸŽ“ Thesis Archive β†—
DNAPLOT & IMGT Genesis
IMGT, the international ImMunoGeneTics database
Giudicelli, V., Chaume, D., Bodmer, J., MΓΌller, W., Busin, C., Marsh, S., Bontrop, R., Marc, L., Malik, A., & Lefranc, M.-P. (1997)
Nucleic Acids Research, 25(1), 206–211
πŸ“„ DOI: 10.1093/nar/25.1.206 β†— πŸ”¬ PubMed: 9016537 β†—
Collier de Perles 2D Layout
IMGT, the international ImMunoGeneTics database (Collier de Perles Graphical Model)
Lefranc, M.-P., Giudicelli, V., Busin, C., Bodmer, J., MΓΌller, W., Bontrop, R., Lemaitre, M., Malik, A., & Chaume, D. (1998)
Nucleic Acids Research, 26(1), 297–303
πŸ“„ DOI: 10.1093/nar/26.1.297 β†— πŸ”¬ PubMed: 9399859 β†—
Numbering System
IMGT unique numbering for immunoglobulin and T cell receptor variable domains and Ig superfamily V-like domains
Lefranc, M.-P., PommiΓ©, C., Ruiz, M., Giudicelli, V., Foulquier, E., Truong, L., Thouvenin-Contet, V., & Lefranc, G. (2003)
Developmental and Comparative Immunology, 27(1), 55–77
πŸ“„ DOI: 10.1016/S0145-305X(02)00039-3 β†— πŸ”¬ PubMed: 12477501 β†—
VBASE Human VH Directory
The repertoire of human germline VH sequences reveals about fifty groups of VH segments with different hypervariable loops
Tomlinson, I. M., Walter, G., Marks, J. D., Llewelyn, M. B., & Winter, G. (1992)
Journal of Molecular Biology, 227(3), 776–798
πŸ“„ DOI: 10.1016/0022-2836(92)90223-7 β†— πŸ”¬ PubMed: 1404389 β†—
Human Repertoire Mapping
The human immunoglobulin VH repertoire
Cook, G. P., & Tomlinson, I. M. (1995)
Immunology Today, 16(5), 237–242
πŸ“„ DOI: 10.1016/0167-5699(95)80166-9 β†— πŸ”¬ PubMed: 7779254 β†—
Murine VH Classification
A new classification of mouse VH sequences
Dildrop, R. (1984)
Immunology Today, 5(4), 85–86
πŸ“„ DOI: 10.1016/0167-5699(84)90034-3 β†— πŸ”¬ PubMed: 25291694 β†—
NP Response & Somatic Mutation
Analysis of somatic mutation and class switching in naive and memory B cells generating adoptive primary and secondary responses
Siekevitz, M., Kocks, C., Rajewsky, K., & Dildrop, R. (1987)
Cell, 48(5), 757–770
πŸ“„ DOI: 10.1016/0092-8674(87)90073-0 β†— πŸ”¬ PubMed: 3493076 β†—
Somatic Hypermutation Review
Stable expression and somatic hypermutation of antibody V regions in B-cell developmental pathways
Kocks, C., & Rajewsky, K. (1989)
Annual Review of Immunology, 7, 537–559
πŸ“„ DOI: 10.1146/annurev.iy.07.040189.002541 β†— πŸ”¬ PubMed: 2653375 β†—
B1-8 Hybridoma Sequencing
Heavy chain variable region contribution to the NPb family of antibodies: somatic mutation evident in a Ξ³2a variable region
Bothwell, A. L. M., Paskind, M., Reth, M., Imanishi-Kari, T., Rajewsky, K., & Baltimore, D. (1981)
Cell, 24(3), 625–637
πŸ“„ DOI: 10.1016/0092-8674(81)90089-1 β†— πŸ”¬ PubMed: 6788376 β†—
Anti-NP Clonal Families
Analysis of the repertoire of anti-NP antibodies in C57BL/6 mice by cell fusion. I. Characterization of antibody families in the primary and hyperimmune response
Reth, M., HΓ€mmerling, G. J., & Rajewsky, K. (1978)
European Journal of Immunology, 8(6), 393–400
πŸ“„ DOI: 10.1002/eji.1830080605 β†— πŸ”¬ PubMed: 97089 β†—
17.2.25 QM Mouse Model
A quasi-monoclonal mouse
Cascalho, M., Ma, A., Lee, S., Masat, L., & Wabl, M. (1996)
Science, 272(5268), 1649–1652
πŸ“„ DOI: 10.1126/science.272.5268.1649 β†— πŸ”¬ PubMed: 8658139 β†—
Monoclonal Antibodies Foundation
Continuous cultures of fused cells secreting antibody of predefined specificity
KΓΆhler, G., & Milstein, C. (1975)
Nature, 256(5517), 495–497
πŸ“„ DOI: 10.1038/256495a0 β†— πŸ”¬ PubMed: 1172191 β†—
AIRR Community Standard
Reproducibility and reuse of Adaptive Immune Receptor Repertoire data
Breden, F., Luning Prak, E. T., Peters, B., et al. & the AIRR Community (2017)
Frontiers in Immunology, 8, 1418
πŸ“„ DOI: 10.3389/fimmu.2017.01418 β†— πŸ”¬ PubMed: 29163494 β†—
AIRR Data Formats
AIRR Community standardized representations for annotated immune repertoires
Vander Heiden, J. A., Marquez, S., et al. & the AIRR Community (2018)
Frontiers in Immunology, 9, 2206
πŸ“„ DOI: 10.3389/fimmu.2018.02206 β†— πŸ”¬ PubMed: 30323809 β†—
OGRDB Inferred Alleles
OGRDB: a framework for community curation of immunoglobulin and T cell receptor germline genes
Lees, W., Busse, C. E., Corcoran, M., Ohlin, M., Ralph, P., Schramm, C. A., Watson, C. T., Breden, F., & Collins, A. M. (2020)
Nucleic Acids Research, 48(D1), D1005–D1010
πŸ“„ DOI: 10.1093/nar/gkz822 β†— πŸ”¬ PubMed: 31566225 β†— 🌐 OGRDB Portal β†—
Observed Antibody Space
Observed Antibody Space: a resource for data mining next-generation sequencing of antibody repertoires
Kovaltsuk, A., Leem, J., Kelm, S., Snowden, J., Deane, C. M., & Krawczyk, K. (2018)
The Journal of Immunology, 201(12), 3694–3702
πŸ“„ DOI: 10.4049/jimmunol.1800708 β†— πŸ”¬ PubMed: 30217829 β†—
Amphibian Immunogenetics
The immune system of Xenopus
Du Pasquier, L., Schwager, J., & Flajnik, M. F. (1989)
Annual Review of Immunology, 7, 251–275
πŸ“„ DOI: 10.1146/annurev.iy.07.040189.001343 β†— πŸ”¬ PubMed: 2653371 β†—
Kabat Framework Foundation
An analysis of the sequences of the variable regions of Bence Jones proteins and myeloma light chains and their implications for antibody complementarity
Wu, T. T., & Kabat, E. A. (1970)
The Journal of Experimental Medicine, 132(2), 211–250
πŸ“„ DOI: 10.1084/jem.132.2.211 β†— πŸ”¬ PubMed: 5508247 β†—
GenBank Public Resource
GenBank: The Nucleotide Sequence Database
Benson, D. A., Cavanaugh, M., Clark, K., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J., & Sayers, E. W. (2013)
Nucleic Acids Research, 41(Database issue), D36–D42
πŸ“„ DOI: 10.1093/nar/gks1195 β†— πŸ”¬ PubMed: 23193287 β†— 🌐 GenBank NCBI β†—