VBASE3 Single-Cell Paired Antibody Repertoire Studio — Industrial Provenance & Analytics

📋 Regulatory & Industrial Metadata Provenance Core

Audit Standard: ISO 8601 UTC • SHA-256 Input Authentication • Research Use Only (RUO)

Sample Identifier

Donor / Patient ID

Study / Dataset Name

Sequencing Platform

VBASE3 Core Release: v1.0.0 (Sept 2026) Analysis Timestamp (UTC): - Input SHA-256: e3b0c44298fc1c149... ℹ️ Research Use Only (RUO) • Regulated use requires independent validation

| Open Literature Presets:

📖 Active Benchmark Open-Source Reference 100% Authentic Open Data CC-BY 4.0

Convergent antibody responses to SARS-CoV-2 in convalescent individuals

Robbiani, D. F., Gaebler, C., Muecksch, F., et al. (2020) • Nature, 584: 437–442 • RCSB PDB 7K8M • GenBank MW040300

🔗 Article DOI ↗ 📦 Primary PDB Accession ↗

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User Repertoire Data Ingestion Client-Side SIMD Engine

Provide your own experimental data via drag-and-drop file upload or direct text paste. Supports AIRR Community TSV, 10x Genomics CellRanger CSV, Simple TSV/CSV, or Paired FASTA. Zero network transmission.

📖 Expected Data Format Specifications & Column Requirements: Click any tab below to review the required columns or copy a ready-to-use sample snippet

AIRR Community standard: Tab-delimited file with one record per contig. Rows sharing the same sequence_id or cell barcode are automatically paired across heavy (IGH/TRB) and light (IGK/IGL/TRA) chains.

sequence_id	v_call	j_call	junction_aa	duplicate_count	locus	timepoint	target
donor_cell_01_H	humIGHV1-69*01	humIGHJ4*01	CARDGYYDILTGYYFDYW	112	IGH	Day 0	Healthy Baseline
donor_cell_01_L	humIGKV1-39*01	humIGKJ1*01	CQQSYSTPPTF	112	IGK	Day 0	Healthy Baseline
donor_cell_02_H	humIGHV1-69*01	humIGHJ6*01	CARDKGYSYGYW	94	IGH	Day 28	SARS-CoV-2 S2
donor_cell_02_L	humIGKV3-20*01	humIGKJ2*01	CQQYGSSPLTF	94	IGK	Day 28	SARS-CoV-2 S2

Required columns: v_call, j_call, junction_aa (CDR3), locus. Optional: duplicate_count, timepoint, target.

10x Genomics CellRanger: Directly drag-and-drop your filtered_contig_annotations.csv file. Contigs sharing the identical barcode are paired into heterodimers.

barcode,chain,v_gene,j_gene,cdr3,reads,productive,is_cell
AAACCTGAGAAACCGA-1,IGH,IGHV1-69,IGHJ4,CARDGYYDILTGYYFDYW,42,True,True
AAACCTGAGAAACCGA-1,IGK,IGKV1-39,IGKJ1,CQQSYSTPPTF,38,True,True
AAACCTGAGAAACCGT-1,IGH,IGHV1-69,IGHJ6,CARDKGYSYGYW,55,True,True
AAACCTGAGAAACCGT-1,IGK,IGKV3-20,IGKJ2,CQQYGSSPLTF,49,True,True

Non-productive contigs (stop codons, frameshifts) are automatically audited and filtered.

Simple Paired Table: Exactly one line per single-cell heterodimer. Perfect for copying and pasting columns from Microsoft Excel, Apple Numbers, or Google Sheets.

cell_id	heavy_v	light_v	heavy_cdr3	light_cdr3	freq	timepoint	target
clone_1	humIGHV1-69*01	humIGKV1-39*01	CARDGYYDILTGYYFDYW	CQQSYSTPPTF	120	Pre-Bleed	Healthy Baseline
clone_2	humIGHV1-69*01	humIGKV3-20*01	CARDKGYSYGYW	CQQYGSSPLTF	85	Day 28	Spike S2 Stem
clone_3	humIGHV3-53*01	humIGKV1-9*01	CARDLDYFDFW	CQQYDTYPLTF	64	Day 7	RBD Class 1
clone_4	humTRBV6-5*01	humTRAV8-4*01	CASSIYSGNTIYF	CAVSDGGSQGNLIF	45	Post-Tx	MAGE-A3 / HLA-A*01

Can be tab-delimited (TSV) or comma-delimited (CSV). Delimiter is auto-detected.

Paired Multi-FASTA: Standard FASTA format where paired chains are identified either sequentially or via header suffixes (>clone1_heavy, >clone1_light, >clone1_H, >clone1_L, or >clone1_TRB / >clone1_TRA). The engine accepts nucleotide DNA in any reading frame (with automated productive frame and mature FR1 anchor detection) or amino acid protein sequences.

>clone1_heavy humIGHV3-23*01
EVQLVESGGGLVQPGGSLRLSCAASGFNIKDTYIHWVRQAPGKGLEWVARIYPTNGYTRYADSVKGRFTISADTSKNTAYLQMNSLRAEDTAVYYCSRWGGDGFYAMDYWGQGTLVTVSS
>clone1_light humIGKV1-39*01
DIQMTQSPSSLSASVGDRVTITCRASQDVNTAVAWYQQKPGKAPKLLIYSASFLYSGVPSRFSGSRSGTDFTLTISSLQPEDFATYYCQQHYTTPPTFGQGTKVEIK

Nucleotide DNA in any reading frame (+0, +1, +2) or amino acid protein sequences are automatically recognized, evaluated, and translated.

📂

Drop Repertoire File Here

or click to browse (.tsv, .csv, .fasta, .txt)

Max recommended file size: 50MB

Or Paste Raw Table / FASTA Content:

Paired Single Cells 645 Productive V_H + V_L Heterodimers

Productive Pairing Rate 98.4% Zero Stop Codons in Frame 0

Expanded Clonotypes 42 Ranked by Cellular Frequency

Mean Somatic Hypermutation 9.2 aa Divergence from VBASE3 Class I Germline

Synthesis Compliance 100.0% Canonical TVSS/VEIK/TVL (Zero Overhang)

Top Expanded Single-Cell Clonotypes

Ranked by cell barcode count with VBASE3 Class I germline assignment, synthesis boundaries, and cohort/timepoint tags

Clone Rank	Cohort / Timepoint	Cell Frequency	Target Antigen	V_H Assignment	J_H Element	CDR-H3 Loop	V_L Assignment	J_L Element	CDR-L3 Loop	SHM (H/L)	Synthesis Boundary

Heavy vs. Light Chain Family Pairing Matrix

Combinatorial pairing rates between V_H families (IGHV1–7) and Light Chain families (IGKV1–6, IGLV1–10)

V_H Family Dominance Frequency (%)

V_L (Kappa vs. Lambda) Usage Ratio Breakdown

🔥 2D V × J Combinatorial Pairing Heatmap Heavy Chain (IGHV × IGHJ)

Contingency matrix showing clone cell frequency and recombination pairing between V and J gene segments.

Chain Target:

Zero (0%)

High Frequency (-)

CDR3 Loop Physicochemical Profiles

Loop length distribution, Kyte-Doolittle hydropathy index, and net charge at pH 7.4

CDR-H3 Loop Length DistributionAmino Acids

CDR-H3 Hydropathy vs. Net ChargeBiophysical Class

Single-Cell Heterodimer PaCMAP Manifold

Joint V_H ⊕ V_L continuous topological embedding with clonal lineage trajectory vectors

ℹ️ Why Arbitrary Units (a.u.)?

Non-linear manifold projections (PaCMAP/UMAP) optimize relative pairwise distance hierarchies rather than absolute Cartesian lengths. Relative distances preserve local sequence neighborhoods and global phylogeny; numerical values on Dimensions 1 & 2 reflect this continuous topology.

⏱️ Longitudinal Somatic Hypermutation Kinetics & Lineage Trajectories Day 0 → Day 180 Monitoring

Quantitative tracking of somatic hypermutation rate, clonal lineage expansion, and affinity maturation trajectories during vaccination or immune interventions.

Somatic Hypermutation Accumulation Curve Mean SHM vs. Time

Lineage Abundance & Clonal Expansion Clonal Frequency (%)

Clonal Lineage Longitudinal Evolution Table

Lineage ID	Founder Precursor (Day 0)	Day 7 Plasmablasts	Day 28 Memory B	Day 180 Booster Recall	Total SHM Accrued	Neutralization Target