IgBLAST Now Available on Vecura

What is IgBLAST?

IgBLAST is NCBI's specialized command-line tool for analyzing immunoglobulin (Ig) and T-cell receptor (TCR) variable-domain sequences. It aligns query sequences against germline V, D, and J gene databases to identify the best-matching gene alleles, delineates framework regions (FWR1-4) and complementarity-determining regions (CDR1-3), and characterizes V(D)J rearrangement junctions. The tool processes both nucleotide sequences (via igblastn) and protein sequences (via igblastp), supporting five species: human, mouse, rat, rabbit, and rhesus monkey.

It helps users assign germline gene calls and map functional regions across antibody and TCR sequences at scale. It is especially useful for characterizing immune repertoires from sequencing data, identifying somatic hypermutation patterns, and preparing sequences for clonotype clustering with downstream tools like Change-O and Immcantation.

What can users do with IgBLAST on Vecura?

With IgBLAST on Vecura, users can:

• Annotate antibody and TCR variable-domain sequences with germline V, D, and J gene assignments
• Delineate framework regions and complementarity-determining regions using IMGT or Kabat numbering schemes
• Characterize V(D)J rearrangement junctions and assess sequence productivity
• Export results in AIRR-compliant TSV format for seamless integration with downstream analysis pipelines

What the output means

The output provides an AIRR Rearrangement-schema table containing germline gene calls (v_call, d_call, j_call, c_call), delineated region sequences (fwr1-4, cdr1-3), junction details (junction, junction_aa, cdr3_aa), productivity assessment (productive, stop_codon, vj_in_frame), and alignment statistics (v_identity, v_score, v_support). Raw IgBLAST output is also available for archival or direct use with AIRR-compliant tools.

This output should be used to support scientific decision making. It does not replace experimental validation.

Why this matters

Antibody and T-cell receptor repertoire analysis is fundamental to understanding adaptive immune responses, developing therapeutic antibodies, and studying immune system diversity. Traditional BLAST tools have limited utility for these sequences because the rearranged nature of immunoglobulin genes and variable gene lengths require specialized alignment strategies. IgBLAST addresses this by providing a unified framework that simultaneously searches germline gene databases, identifies the contributing V, D, and J segments, and maps functional domains critical for antigen binding.

The adoption of AIRR (Adaptive Immune Receptor Repertoire) Community standards ensures interoperability across the immunology research ecosystem. By producing AIRR-compliant output, IgBLAST enables researchers to feed results directly into established analysis pipelines for clonotype clustering, lineage tracing, and repertoire comparison—accelerating discoveries in vaccine development, autoimmune disease research, and cancer immunotherapy.

• Developed by: NCBI (National Center for Biotechnology Information)
• Source: NCBI IgBLAST Documentation | GitHub Repository
• Reference: Ye, J., Ma, N., Madden, T.L., & Ostell, J.M. (2013). IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Research, 41(Web Server issue), W340-5. PubMed