VaxPress is a powerful codon optimization tool designed specifically for mRNA vaccine development. It uses various biological factors such as iCodon stability, Codon Adaptation Index (CAI), U count minimization, RNA folding, GC ratio, and tandem repeats to optimize codon usage, aiming to enhance mRNA stability, translation efficiency, and immunogenicity.
You can install VaxPress via pip:
pip install vaxpressconda install -c conda-forge -c bioconda -c changlabsnu vaxpressFirst, you will need to install Singularity CE. Once Singularity is installed, you can download the VaxPress image from our GitHub repository and run using the following command:
singularity vaxpress.sif ...vaxpress -i INPUT -o OUTPUTFor more detailed usage instructions including all the available options, please refer to the usage guide.
These options include input fasta file, whether input is a protein sequence, output directory, etc.
These options include preset values, number of processes, random seed, target species, etc.
These options include number of iterations, offsprings per iteration, survivors per iteration, initial mutation rate, etc.
These options include scoring weights for iCodon predicted stability, CAI, bicodon-weight, U count minimizer, RNA folding, GC ratio, tandem repeats, etc.
This project is licensed under the MIT License.
If you have any questions or feedback, please feel free to contact us.