Amulety
Amulety stands for Adaptive imMUne receptor Language model Embedding tool for TCR and antibodY. Amulety is a Python command line tool to embed B-cell receptor (BCR), also termed antibodies in their secreted form, and T-cell receptor (TCR) amino acid sequences using pre-trained general protein or specific immune receptor language models. The package supports both BCR and TCR embeddings. The package also has functionality to translate nucleotide sequences to amino acids with IgBlast.
Contact
If you need help or have any questions, please contact the Immcantation Group.
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Citing
If you use this package, please cite the pre-print:
AMULETY: A Python package to embed adaptive immune receptor sequences. Meng Wang, Yuval Kluger, Steven H. Kleinstein, Gisela Gabernet. BioRXiv 2025. DOI: https://doi.org/10.1101/2025.03.21.644583
To cite the paper comparing the embedding methods on BCR sequences, please cite:
Supervised fine-tuning of pre-trained antibody language models improves antigen specificity prediction. Meng Wang, Jonathan Patsenker, Henry Li, Yuval Kluger, Steven H. Kleinstein. BioRXiv 2024. DOI: https://doi.org/10.1101/2024.05.13.593807.
License
This project is licensed under the terms of the GPL v3 license.