---
title: IgBLAST on the platform
description: >-
  Assign the germline V gene and count framework mutations from germline
  (somatic hypermutation) for amino-acid antibody sequences with IgBLAST.
tags:
  - igblast
  - antibodies
---

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](/docs/antibodies) 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](/docs/anarci).

## Try it

**Try this prompt** — [open in a guest chat](/chat/new?guest=true&prompt=Run%20IgBLAST%20on%20the%20adalimumab%20heavy-chain%20amino-acid%20sequence%20to%20assign%20its%20germline%20V%20gene%20and%20count%20its%20framework%20mutations%2C%20then%20score%20joint%20VH%2FVL%20humanness%20with%20Humatch%20%E2%80%94%20does%20the%20fully%20human%20antibody%20score%20above%20therapeutic%20threshold%2C%20and%20recommend%20whether%20the%20V-gene%20assignment%20suggests%20a%20manufacturer-specific%20humanization%20liability%20for%20a%20biosimilar%20program%3F).

> Run IgBLAST on the adalimumab heavy-chain amino-acid sequence to assign its germline V gene and count its framework mutations, then score joint VH/VL humanness with Humatch — does the fully human antibody score above therapeutic threshold, and recommend whether the V-gene assignment suggests a manufacturer-specific humanization liability for a biosimilar program?

_IgBLAST assigns the germline V gene; Humatch scores humanness — a common annotate-then-score pair._

## 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](https://doi.org/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](/docs/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](/docs/anarci) instead when you need a specific numbering scheme (IMGT, Kabat, Chothia) rather than germline gene hits. Reach for [Humatch](/docs/humatch) or [BioPhi](/docs/biophi) when the question is humanness. IgBLAST chains forward into [Humatch](/docs/humatch) scoring, [ANARCI](/docs/anarci) numbering, and [antibody developability](/docs/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