How does MiXCR recognize CDR3 and by which conserved amino acids?

[linxianzu1995]

IMGT

A JUNCTION begins at the second conserved cysteine of the V-REGION (2nd-CYS), at position 104 according to the IMGT unique numbering (Lefranc et al., 2003b). A JUNCTION ends with the conserved tryptophan (J-TRP, for the IGH chains) or the conserved phenylalanine (J-PHE, for the IG light chains and the TR chains) at position 118 according to the IMGT unique numbering (Lefranc et al., 2003b)

issue

Checking the output clonotype results, the starting amino acids recognized for CDR3 are Cyc(C), Gly(G), Asp(D), Arg(R), Ser(S), etc. Are these the starting amino acids that MiXCR uses to recognize CDR3?

[PoslavskySV]

Hi, it is probably related to this discussion as well. @Alex-Davydov could you elaborate please?

[Alex-Davydov]

Hi,
Mixcr reference contains all coordinates of the beginning of frameworks and cdrs for V genes (L1, L2, FR1, CDR1, FR2, CDR2, FR3, CDR3) and J genes (JBegin, FR4Begin and FR4End), so the CDR3 region is defined as an nucleotide sequence between CDR3Begin point in V gene and FR4Begin in J gene. The CDR3Begin is the first nucleotide of the codon which encodes conservative cysteine and FR4Begin is the nucleotide right after the triplet which encodes tryptophan or phenylalanine (mixcr works on nucleotides level). More information about the format of mixcr reference libraries you can find here.

[linxianzu1995]

Hi, As there is no detailed description of the recognition of CDR3 in the align step, only the algorithm for align is described. can you explain the workflow of MiXCR for CDR3 recognition?