IgBLAST on the platform
Assign the germline V gene and count framework mutations from germline (somatic hypermutation) for amino-acid antibody sequences with IgBLAST.
Every antibody is built from germline V, D, and J gene segments that then hypermutate as the immune response matures. Knowing which segments built a given sequence — and how far it has drifted from them — tells you its lineage, its likely humanness liabilities, and where its diversity lives. On this platform IgBLAST assigns the germline V gene and counts the framework mutations, for amino-acid antibody sequences. It is the germline-analysis half of the antibody engineering numbering step.
Known accuracy issue
IgBLAST can return incorrect germline V gene assignments while the job still reports status SUCCESS. Verify a germline call against an independent source before relying on it for lineage or humanization decisions.
V only, and protein only
D and J genes are not assigned, and the CDR3 is not named. This platform runs igblastp, which takes a V germline database and nothing else, so IgBLAST makes no D or J assignment for an amino-acid query and reports only the germline-encoded end of the CDR3 — not the real one. Nucleotide input is not accepted: the nucleotide databases are not installed, so a nucleotide sequence is refused rather than analysed. For CDR3 and region boundaries use ANARCI.
Try it
What IgBLAST does
IgBLAST aligns an antibody sequence against germline immunoglobulin gene databases to identify the gene segments that recombined to form it. Here it reports the top V hits with alignment statistics and measures how many framework mutations have accumulated (somatic hypermutation).
⊘ What the upstream tool can do but this deployment does not. IgBLAST itself assigns V, D and J, names the junction and flags productivity — but that requires igblastn on a nucleotide sequence with V, D and J germline databases installed. This deployment runs igblastp with a V database only, so D and J are never searched, the junction is not resolved, and productivity is not determined. A result therefore distinguishes "not searched" from "searched and not found"; it never substitutes one for the other.
Citations
Ye J, Ma N, Madden TL, Ostell JM. IgBLAST: an immunoglobulin variable domain sequence analysis tool. Nucleic Acids Research. 2013;41(W1):W34-W40. doi: 10.1093/nar/gkt382
When to reach for it
- V gene assignment — you want the germline V gene that built the sequence, with alignment statistics. ⊘ For D and J, or for the real CDR3, this is not the tool.
- Amino-acid input — you have the protein sequence or a therapeutic name, not the nucleotide sequence. ⊘ For CDR and framework boundaries, use ANARCI.
- Germline alignment — you want the closest germline gene hits ranked by identity and E-value.
- Somatic hypermutation analysis — you want to know how far the sequence has drifted from germline.
Reach for ANARCI instead when you need a specific numbering scheme (IMGT, Kabat, Chothia) rather than germline gene hits. Reach for Humatch or BioPhi when the question is humanness. IgBLAST chains forward into Humatch scoring, ANARCI numbering, and antibody developability.
How it fits the workflow
IgBLAST is an annotation step. A typical arc is OAS search → IgBLAST annotation → Humatch scoring: mine natural repertoires, annotate the germline lineage of the hits, then score humanness. Because it accepts a therapeutic name, you can also start from a known therapeutic and let the platform resolve the VH/VL from Thera-SAbDab. Each run takes one antibody name, so a multi-antibody panel needs one run per antibody.
How it runs
IgBLAST runs as an asynchronous CPU job on Modal compute. You submit one or more sequences, the platform tracks and polls the job, and a result card lands on the canvas when it finishes — typically within seconds to a minute.
Read next
Was this page helpful?