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CodonTransformer

Optimize codon usage for protein sequences across 164 organisms.

  • Paper: Nature Communications 2025
  • Upstream: https://github.com/Adibvafa/CodonTransformer
  • License: Apache 2.0
  • Device: CPU or GPU. Two image variants:
    • rnazoo-codontransformer:latest — CUDA-enabled (default, used with -profile gpu)
    • rnazoo-codontransformer-cpu:latest — CPU-only (smaller, used with -profile cpu)

What it does

CodonTransformer uses a BigBird transformer model to optimize codon usage for a given protein sequence and target organism. It takes amino acid sequences as input and outputs DNA coding sequences with optimized codons for expression in the target organism. Supports 164 organisms.

Input format

FASTA file of amino acid sequences:

>test_protein_1
MALWMRLLPLLALLALWGPDPAAAFVN
>test_protein_2
MKWVTFISLLFLFSSAYS

Output format

FASTA file of optimized DNA coding sequences (includes start and stop codons):

>test_protein_1
ATGGCCCTGTGGATGAGGCTGCTGCCCCTGCTGGCCCTGCTGGCCCTGTGGGGCCCTGACCCTGCTGCCGCCTTTGTGAACTGA
>test_protein_2
ATGAAGTGGGTGACCTTTATCTCTCTGCTGTTCCTGTTCTCTTCTGCCTACAGCTGA

Run with Docker

See the Direct Docker guide for the shared docker run recipe (UID, HOME, USER env vars, and GPU flag). Below are the model-specific parts.

# CPU
docker run --rm \
  -v /path/to/input.fa:/data/input.fa \
  -v /path/to/output:/out \
  ghcr.io/ericmalekos/rnazoo-codontransformer-cpu:latest \
  codon_transformer_predict.py \
    -i /data/input.fa \
    -o /out/optimized_codons.fa \
    --organism "Homo sapiens"

# GPU
docker run --rm --runtime=nvidia -e NVIDIA_VISIBLE_DEVICES=all \
  -v /path/to/input.fa:/data/input.fa \
  -v /path/to/output:/out \
  ghcr.io/ericmalekos/rnazoo-codontransformer:latest \
  codon_transformer_predict.py \
    -i /data/input.fa \
    -o /out/optimized_codons.fa \
    --organism "Homo sapiens"

Run with Nextflow

# CPU
nextflow run main.nf -profile docker,cpu \
  --codontransformer_input /path/to/input.fa \
  --codontransformer_organism "Homo sapiens"

# GPU
nextflow run main.nf -profile docker,gpu \
  --codontransformer_input /path/to/input.fa \
  --codontransformer_organism "Homo sapiens"

Only models with input provided will run — no ignore flags needed.

Parameters

Parameter Default Description
--codontransformer_organism Homo sapiens Target organism (any of 164 supported organisms)

Supported organisms (partial list)

Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, Drosophila melanogaster, Caenorhabditis elegans, Saccharomyces cerevisiae, Escherichia coli, Arabidopsis thaliana, and 155 more.

See the full list at https://github.com/Adibvafa/CodonTransformer.

Example

Input: 

>insulin_fragment
MALWMRLLPLLALLALWGPDPAAAFVN

Output: 

>insulin_fragment
ATGGCCCTGTGGATGAGGCTGCTGCCCCTGCTGGCCCTGCTGGCCCTGTGGGGCCCTGACCCTGCTGCCGCCTTTGTGAACTGA

The optimized DNA sequence encodes the same protein but uses codons preferred by the target organism for improved expression.