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How to infer CDR1, CDR2, and CDR3 sequences from a TCR chain protein sequence?

How can one infer the CDR1, CDR2, and CDR3 sequences of a T cell receptor (TCR) protein given its amino acid sequence like the one below?

KTTQPPSMDCAEGRAANLPCNHSTISGNEYVYWYRQIHSQGPQYIIHGLKNNETNEMASLIITEDRKSSTLILPHATL
DTAVYYCIVVRSSNTGKLIFGQGTTLQVKPDIQNPDPAVYQLRDSKSSDKSVCLFTDFDSQTNVSQSKDSDVYITDKCV
DMRSMDFKSNSAVAWSNKSDFACANAFNNSIIPEDTFFPS

I'm looking for suggestions on computational tools and methods that can be used to identify the V, D, and J gene segments and determine the boundaries of the CDRs regions.

Any help would be greatly appreciated. Thank you!

tcr cdr2 cdr3 vdj cdr1
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written by nomorewords • nomorewords

1 answer

IgBLAST (despite the name) can annotate TCR sequences with details like germline gene usage and CDR/FWR regions for human and mouse sequences. Just select the "Analyze T cell receptor (TR) sequences" tab and, if you're searching protein sequences like in this example, set the program to "blastp" instead of "blastn." There's also a command-line version (use -ig_seqtype TCR with that).

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written by Jesse • Jesse

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