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melihyilmaz avatar melihyilmaz commented on July 3, 2024

Hi,

Thanks for pointing out that it was unused, I will remove it from the config template.

The pre-trained models are trained to decode peptides from C-terminus to N-terminus (right to left) as this is likely marginally easier since there are fewer possible amino acids at the C-terminus for tryptic peptides. So by default, the raw model output sequences are reversed to get the correct ordering of amino acid in the peptide.

from casanovo.

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