Apply tcr-dist on amino acid sequences

[rx-li]

Hello,

Thanks for developing such great tools!

I am wondering if there is a way to apply tcr-dist on cdr3 amino acid sequences.
Currently, the instructions say it is required "nucleotide sequences of the TCR alpha and beta chain reads". However, we got a dataset with amino acid sequences instead of nucleotide sequences and would like to try your methods.

Thanks so much for your help in advance!

Best regards,
Ruoxing

[phbradley]

Hi Ruoxing, Thanks for your interest! I would recommend instead using the new tcrdist3 tool which is better documented and actively supported. https://github.com/kmayerb/tcrdist3 For calculating TCRdist distances you do not need CDR3 nucleotide sequences, but you will need V gene identifiers. Take care, Phil

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________________________________ From: Ruoxing Li ***@***.***> Sent: Tuesday, July 18, 2023 11:53 AM To: phbradley/tcr-dist ***@***.***> Cc: Subscribed ***@***.***> Subject: [phbradley/tcr-dist] Apply tcr-dist on amino acid sequences (Issue #44) CAUTION: This email originated from outside of the organization. Do not click links or open attachments unless you recognize the sender and know the content is safe. Hello, Thanks for developing such great tools! I am wondering if there is a way to apply tcr-dist on cdr3 amino acid sequences. Currently, the instructions say it is required "nucleotide sequences of the TCR alpha and beta chain reads". However, we got a dataset with amino acid sequences instead of nucleotide sequences and would like to try your methods. Thanks so much for your help in advance! Best regards, Ruoxing — Reply to this email directly, view it on GitHub<https://urldefense.com/v3/__https://github.com/phbradley/tcr-dist/issues/44__;!!GuAItXPztq0!j0swr4KFDo0q0eDV1ct_NuU3pNPpK3OsvmJx1H9MIM5qJ-pfcPV8jHATSPOIuSV0c2lFJhX9XA9IFt7t26ZL_0wH$>, or unsubscribe<https://urldefense.com/v3/__https://github.com/notifications/unsubscribe-auth/ABBNCH47W4A2X5GRBM2Y263XQ3LRLANCNFSM6AAAAAA2OZ7ZLM__;!!GuAItXPztq0!j0swr4KFDo0q0eDV1ct_NuU3pNPpK3OsvmJx1H9MIM5qJ-pfcPV8jHATSPOIuSV0c2lFJhX9XA9IFt7t2wBTGweJ$>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>