stitchr

Stitch together TCR coding nucleotide sequences from V/J/CDR3 information

Contents:

• Getting started
  • Installation
  • Quick start example
• Using stitchr
  • Gene/allele default behaviour
  • Translation sequences
  • Seamless mode
  • Other optional arguments
    • Output modes
    • Providing a partial amino acid sequence
  • A note on CDR3 C-terminal residues
• stitchr input data
  • Species covered
  • Generating new IMGT input files
  • Stitchr data formatting
    • Codon usage files
    • Preferred allele files
    • Skipping constant region checks
• Thimble
  • Run stitchr high-throughput on multiple and paired TCRs
    • Example usage
  • Optional arguments
• GUI-stitchr
• Stitching immunoglobulins
• Importing stitchr for use in other Python scripts
• stitchr warnings
• Citing stitchr
• Licensing information

Sometimes you need a complete TCR nucleotide or amino acid sequence, but all you have is limited information. This script aims to generate a coding nucleotide sequence for a given rearrangement (e.g. for use when generating TCR expression vectors) in those situations.

The script takes the known V/J/CDR3 information, and uses that to pull out the relevant germline TCR nucleotide sequences and stitch them together. Its modular approach can be used for the automated generation of TCR sequences for gene synthesis and functional testing, or for TCR engineering through supplying modified germline sequences.

Out of the box, stitchr works on all common jawed vertebrate TCR loci (alpha/beta/gamma/delta), for all species for which there is currently data available in IMGT.

Links

• stitchr on GitHub

• stitchr on PyPI