IgBLAST inputs and parameters
Sequences, organism, domain system, and alignment options for IgBLAST.
You provide one or more antibody sequences and choose the organism whose germline database IgBLAST should align against. The organism is the parameter that matters most: aligning a mouse antibody against the human database mislabels every germline gene. Everything else tunes how many hits you see and how strict the alignment is.
Sequences
IgBLAST accepts a list of antibody variable-region amino-acid sequences. Submit between one and 50 sequences per job.
⊘ Nucleotide input is not accepted. The nucleotide germline databases (V, D and J) are not installed, so a nucleotide sequence is refused rather than analysed. This also means D and J genes are never assigned and the CDR3 is not named — igblastp searches a V database only. Use ANARCI for CDR3 and region boundaries.
sequencesstring[]requiredAntibody variable-region amino-acid sequences. One to 50 per job.
sequence_namesstring[]Optional names for each sequence.
Germline database
organismstringdefault: humanSpecies whose germline database to align against: human, mouse, rat, or rabbit.
domain_systemstringdefault: imgtNumbering / domain system for boundaries: imgt or kabat.
Alignment tuning
num_alignments_vintdefault: 5Number of top V-gene alignments to report (1–20).
num_alignments_jintdefault: 5Number of top J-gene alignments to report (1–20).
evalue_thresholdfloatdefault: 1.0E-value threshold for reporting hits (greater than 0, up to 100).
From a therapeutic name
The igblast_annotate tool also accepts a therapeutic_name — name a known antibody and the platform resolves its VH/VL from Thera-SAbDab before annotating. Submit one name per call; for a multi-antibody panel, make separate parallel calls.
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