IgBLAST outputs and interpretation
Germline V gene hits and framework-mutation counts from IgBLAST, for amino-acid antibody sequences.
IgBLAST returns, per amino-acid sequence, the ranked V germline gene hits with alignment statistics, the top V gene, its percent identity, the chain type, and the number of framework mismatches against germline (somatic hypermutation). D and J are not searched, and the CDR3, productivity and stop-codon status are not determined; each of those fields is null and its reason is listed under undetermined. Read the top V gene and its identity first: a low V-identity means the sequence has hypermutated far from germline, which is exactly what humanness scoring will care about.
Per-sequence result
Each annotated sequence carries these fields:
| Field | Type | What it tells you |
|---|---|---|
sequence_name | string | The name you gave the sequence. |
chain_type | VH | VK | VL | null | Heavy, kappa-light, or lambda-light. |
v_gene_hits | list | Ranked V-gene hits, each with gene_name, identity_pct, evalue, score, alignment_length. |
d_gene_hits | list | Ranked D-gene hits (same shape). ⊘ Always empty here: D is not searched. |
j_gene_hits | list | Ranked J-gene hits (same shape). ⊘ Always empty here: J is not searched. |
top_v_gene | string | null | The best-scoring V gene. |
top_d_gene | string | null | The best-scoring D gene. ⊘ Always null here. |
top_j_gene | string | null | The best-scoring J gene. ⊘ Always null here. |
v_identity_pct | float | null | Percent identity of the top V-gene alignment. |
cdr3_sequence | string | null | The CDR3 amino-acid sequence. ⊘ Always null here: the CDR3 end needs the J gene. |
cdr3_length | int | null | Length of the CDR3. ⊘ Always null here. |
framework_mutations | int | null | Amino-acid mismatches against the germline V gene in the framework regions (somatic hypermutation). |
productive | bool | null | Whether the rearrangement is productive. ⊘ Always null here. |
stop_codon | bool | null | Whether a stop codon was detected. ⊘ Always null here. |
segments_searched | string[] | The germline segments searched: ["V"]. |
undetermined | object | For each field above that is null or empty, the reason it was not determined. |
Job-level summary
| Field | Type | Meaning |
|---|---|---|
failed_sequences | string[] | Sequences IgBLAST could not annotate. |
success_count | int | Sequences annotated successfully. |
fail_count | int | Sequences that failed. |
organism | string | Germline database used. |
domain_system | string | Domain system applied (imgt or kabat). |
sequence_type | protein | The input type the job ran. ⊘ Always protein on this platform — nucleotide input is refused, so nucleotide is never returned. |
Reading the result card
The IgBLAST result renders on the canvas as an antibody-structure annotation card, surfacing the top V gene and its identity so you can read the germline lineage at a glance.
What to do next
- A low
v_identity_pctor highframework_mutationsflags a hypermutated sequence — send it to Humatch or BioPhi for humanness scoring. - Get the CDR3 and region boundaries from ANARCI, then use the CDR3 for repertoire mining with OAS search.
- Number the sequence to a canonical scheme with ANARCI.
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