Crate immunum 

High-performance antibody and TCR sequence numbering.

immunum numbers antibody and T-cell receptor (TCR) variable domain sequences using Needleman-Wunsch semi-global alignment against position-specific scoring matrices (PSSM) built from consensus sequences with BLOSUM62 substitution scores. Chain type is detected automatically by aligning against all requested chains and selecting the best match.

Supported chains and schemes

Chain	Type	Schemes
IGH	Antibody heavy	IMGT, Kabat
IGK	Antibody kappa	IMGT, Kabat
IGL	Antibody lambda	IMGT, Kabat
TRA	TCR alpha	IMGT
TRB	TCR beta	IMGT
TRG	TCR gamma	IMGT
TRD	TCR delta	IMGT

Quick start

use immunum::{Annotator, Chain, Scheme};

// Create an annotator for all antibody chains with IMGT numbering
let annotator = Annotator::new(&[Chain::IGH, Chain::IGK, Chain::IGL], Scheme::IMGT, None).unwrap();

let sequence = "QVQLVQSGAEVKRPGSSVTVSCKASGGSFSTYALSWVRQAPGRGLEWMGGVIPLLTITNYAPRFQGRITITADRSTSTAYLELNSLRPEDTAVYYCAREGTTGKPIGAFAHWGQGTLVTVSS";
let result = annotator.number(sequence).unwrap();

println!("Chain:      {}", result.chain);       // IGH
println!("Confidence: {:.2}", result.confidence);

// Iterate over (amino acid, IMGT position) pairs
for (aa, pos) in sequence.chars().zip(result.positions.iter()) {
    println!("{aa} -> {pos}");
}

Key types

• Annotator — main entry point; holds loaded scoring matrices and numbers sequences
• NumberingResult — the output of Annotator::number: positions, chain, confidence
• Position — an IMGT/Kabat position such as 111 or 111A
• Chain — chain type (IGH, IGK, IGL, TRA, TRB, TRG, TRD)
• Scheme — numbering scheme (IMGT or Kabat)

Modules

• annotator — high-level annotation API
• alignment — Needleman-Wunsch semi-global alignment
• numbering — IMGT and Kabat numbering rules
• scoring — position-specific scoring matrices
• io — FASTA parsing and TSV/JSON/JSONL output
• types — core domain types
• error — error types

Re-exports

pub use numbering::imgt;

pub use numbering::kabat;

pub use alignment::align;

pub use alignment::Alignment;

pub use annotator::Annotator;

pub use annotator::NumberingResult;

pub use annotator::SegmentResult;

pub use annotator::DEFAULT_MIN_CONFIDENCE;

pub use error::Error;

pub use error::Result;

pub use scoring::ScoringMatrix;

pub use types::Chain;

pub use types::Insertion;

pub use types::NumberingRule;

pub use types::Position;

pub use types::Region;

pub use types::Scheme;

pub use io::read_fasta;

pub use io::read_input;

pub use io::NumberedRecord;

pub use io::OutputFormat;

pub use io::Record;

pub use validation::load_validation_csv;

pub use validation::validate_entry;

pub use validation::ValidationEntry;

pub use validation::ValidationResult;

Modules

alignment

Sequence alignment using Needleman-Wunsch algorithm

annotator

High-level API for sequence annotation and chain detection

error

Error types for immunum

io

Input parsing and output formatting for sequence records

numbering

scoring

Scoring matrices for sequence alignment

types

Core types for sequence numbering

validation

Validation against numbered test data