If, like me, you
work on T cell receptors, occasionally you’re probably going to want to
express a particular TCR in cells. However you're not always going to have the
sequence, at either nucleotide or protein sequence level.
Not a problem, you
can sort this out. You can look up all the relevant germline
sequences from IMGT, trim away all the non-used bits, add in
the non-templated stuff, then manually stitch it all together and
have a look to see if it still makes what you were expecting. You can
do all that... or you can just use the code I wrote.
StiTChR
does it all: give it a V gene, a J gene, and a CDR3 amino acid sequence and it'll look up,
trim and stitch together all the relevant TCR nucleotide sequences
for you, back-translating the non-templated region using the most frequent codon per residue. It also translates it all, and will run a quick rudimentary
alignment against a known partial protein sequence if you have one for a visual confirmation that it's made the right thing.
You
can then take the alpha/beta TCR sequences it generates, bang them
into an expression vector (typically split by a T2A sequence or
something) and transduce your cells of interest.
I wrote this code to
save me a bit of time in future, but hopefully it can do the same for
some of you!
