Aligns the CDR3 nucleotide sequence against germline V and J sequences to identify trimming, N-insertion lengths, and D-gene usage (beta only).
Usage
.analyze_junction(
organism,
v_gene,
j_gene,
cdr3_protseq,
cdr3_nucseq,
force_d_id = 0L,
mismatch_score = .DEFAULT_MISMATCH_SCORE_JUNCTION_ANALYSIS
)Arguments
- organism
Character string. Organism identifier.
- v_gene
Character string. V-gene identifier including allele.
- j_gene
Character string. J-gene identifier including allele.
- cdr3_protseq
Character string. CDR3 amino acid sequence.
- cdr3_nucseq
Character string. CDR3 nucleotide sequence (lowercase).
- force_d_id
Integer. If non-zero, only consider this D-gene ID.
- mismatch_score
Integer. Score for a mismatch.