Pseudo-Sequence Alignment
Aligns paratope amino acid sequences using the IMGT numbering scheme to produce standardized pseudo-sequences for downstream analysis
Web app slug: pseudo-sequence-alignment
When to use
Section titled “When to use”Use this pipeline:
- When you have AIRR files and need to generate aligned paratope sequences
Submitting a job
Section titled “Submitting a job”Navigate to Dashboard → Pseudo-Sequence Alignment → Create New Job.
Required inputs
Section titled “Required inputs”| Field | Description |
|---|---|
| Job name | A label for this run |
| Chain Type | The type of immune receptor chain (e.g., TRA, TRB, IGH) |
| Species | The species of the immune receptors (e.g., Human, Mouse) |
| Input Column Name | The name of the column containing amino acid sequences to align |
| Output Column Name | The name of the column to store the aligned pseudo-sequences |
| Bit Score Threshold | The minimum bit score for a valid alignment |
| Assign Germline | Whether to assign germline sequences to the aligned pseudo-sequences |
Troubleshooting
Section titled “Troubleshooting”High fraction of unaligned sequences
Check that the input_column exists in your AIRR files. Run head -1 file.tsv to list columns. Also verify that sequences in that column are amino acids (not nucleotides).
Output column already exists
The processor will overwrite the existing column. If this is unintended, change the output_col parameter to a new name.