Entering edit mode
3.8 years ago
zizigolu
★
4.3k
Hi
I have CDR3 sequences of a patient like below
CASSYLPGQGDHYSNQPQHF
CASSFEAGQGFFSNQPQHF
CASSFEPGQGFYSNQPQHF
CASSYEPGQVSHYSNQPQHF
CASSALASLNEQFF
CASSYLPGQGDHYSNQPQHF
CASSFEAGQGFFSNQPQHF
CASSFEPGQGFYSNQPQHF
CASSYEPGQVSHYSNQPQHF
CASSYLPGQGDHYSNQPQHF
CASSFEAGQGFFSNQPQHF
CASSFEPGQGFYSNQPQHF
CASSYEPGQVSHYSNQPQHF
CASSYLPGQGDHYSNQPQHF
CASSFEAGQGFFSNQPQHF
CASSFEPGQGFYSNQPQHF
CASSYEPGQVSHYSNQPQHF
CASSFGVEDEQYF
How I can find their matched epitope/peptide?
Lets say FLKEKGGL
which is attached to CASSYLPGQGDHYSNQPQHF
Can you clarify the context? What is CDR3 and what matched epitope are you referring to?
The CDR3 region is the preferential target of many T cell receptor (TCR) repertoire studies, due to its relevance for TCR-peptide interaction
I have amino acid sequence of CDR3 and I want to they would attached to which epitope/peptide (antigen)
This is not really my area of expertise, so I'll bow out to others more qualified, but based on experience with MHC peptide presentation etc., as far as I know these types of interaction are not well understood and even harder to predict.
I wouldn't be surprised if there is not an answer to this question (certainly not an easy one).