Getting matched peptide to CDR3 sequences
0
0
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

RNA-Seq • 688 views
ADD COMMENT
0
Entering edit mode

Can you clarify the context? What is CDR3 and what matched epitope are you referring to?

ADD REPLY
0
Entering edit mode

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)

ADD REPLY
1
Entering edit mode

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).

ADD REPLY

Login before adding your answer.

Traffic: 1959 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6