how to identify CDR after numbering sequence

[renyongzhe]

Hi ,all.
Because SCALOP will miss H-CDR3, is there annother tool could identify CDR region? After numbering the antibody sequence, whether it's the right way to extract CDR region according to the position of CDR Definitions ? Any other suggestions would be appreciated.

[gciaberi]

Once you have the numbered antibody sequence then you can simply extract the residues with a number that is within the CDR3 limits given in the definition table you linked to, so something like
[residue for residue, resi in numbered_residues if CDR3_start_index <= resi <= CDR3_end_index].

You just have to be careful to correctly catch residues that have a letter collated to their residue number. Suppose you have an IMGT numbered heavy chain sequence with the following format:
'[... (T, 93), (S, 94), (D, 94A), (H, 94B), (K, 95), ...]

Then you have to make sure you correctly extract the D and H and get TSDHK...

Other than that I don't think there are other edge cases to deal with, maybe just check that the CDR3 sequence you have extracted has a minimum length of 5 or something like that.

[renyongzhe]

Thanks for your interpretation. Annother format in IMGT numbered heavy chain sequence like below where CDR1 located in H26-H33. How to get the correct CDR1 sequence? The output of SCALOP is GFSINGSW.
[(26, S), (27, G), (28, F), (29, S), (30, I), (31, -), (32, -), (33, -), (34, -), (35, N), (36, G), ...]

[gciaberi]

You should double check the CDR definitions table you are using because it seems wrong, in the official IMGT website the CDR1 is defined as H27-38.

[renyongzhe]

You should double check the CDR definitions table you are using because it seems wrong, in the official IMGT website the CDR1 is defined as H27-38.

You are right. But that make me confused about this definitions which many people and documents cite it.