oxpig / CaLM

Protein language model trained on coding DNA

CaLM

The Codon adaptation Language Model

This repository encapsulates all code required to reproduce the results of the paper "Codon language embeddings provide strong signals for use in protein engineering", by Carlos Outeiral and Charlotte M. Deane.

Citation

If you use our work, please cite:

Outeiral, Carlos, and Charlotte M. Deane. Codon language embeddings provide strong signals for use in protein engineering Nature Machine Intelligence 6.2 (2024): 170-179.

Installation

git clone https://github.com/oxpig/CaLM
python setup.py install

Usage

from calm import CaLM

model = CaLM()
model.embed_sequence('ATGGTATAGAGGCATTGA')