TCR to Amino Acid Sequence
Assembles full germline amino acid sequences from V/J gene calls and CDR3 sequences
Web app slug: tcr-to-amino-seq
When to use
Section titled “When to use”Use this pipeline when you have TCR columns like cdr3, V gene and optional J gene, and the goal is to generate the full amino acid sequence.
Web App: Submitting a job
Section titled “Web App: Submitting a job”Navigate to Dashboard → TCR to Amino Acid → New Job.
Required inputs
Section titled “Required inputs”| Field | Description |
|---|---|
| Job name | A label for this run |
| Input file | TSV or CSV file with a nucleotide sequence column and a sequence ID column |
| Nucleotide column | Column name containing nucleotide sequences |
| ID column | Column name containing sequence identifiers |
Optional inputs
Section titled “Optional inputs”| Field | Default | Description |
|---|---|---|
| Reading frame | auto-detect | Force reading frame (0, 1, or 2). Leave blank to auto-detect from the first in-frame codon. |
| Include stop codons | false | If true, translation continues past stop codons (marked with *) |
Output files
Section titled “Output files”| File | Description |
|---|---|
translated_sequences.tsv | Input TSV with added amino_acid_sequence column |
translation_report.json | Statistics (total sequences, successful translations, stop codon count) |
Troubleshooting
Section titled “Troubleshooting”Many sequences have stop codons
This usually means the reading frame is off. Try specifying each frame (0, 1, 2) and check which produces the fewest stop codons.
Invalid nucleotide characters
The validator accepts A, T, G, C, N. Other characters (e.g., IUPAC ambiguity codes like R, Y) will cause validation failure. Pre-process your sequences to replace ambiguous positions with N.