VaxPress

VaxPress is a codon optimizer platform tailored for mRNA vaccine development. It refines coding sequences starting from protein or RNA sequences to boost both storage stability and in vivo protein expression. Plus, additional properties can be easily programmed into the optimization process with just a few lines of code via a pluggable interface. For the detailed information about VaxPress, including its options and algorithmic features, please refer to the VaxPress documentation page.

Installation

pip

You can install VaxPress via pip:

# To install using pip
pip install vaxpress

# To install using pip with LinearFold (only for non-commercial uses)
pip install 'vaxpress[nonfree]'

# To install from the GitHub
git clone https://github.com/ChangLabSNU/VaxPress.git
cd VaxPress
pip install .

Conda

Alternatively, you may also install VaxPress via a conda package:

conda install -c changlabsnu -c bioconda -c conda-forge vaxpress

Singularity

First, you will need to install Singularity CE. Once Singularity is installed, you can download the VaxPress image from this GitHub repository and run using the following command:

singularity vaxpress.sif ...

Usage

Quick Start

Here's a basic command-line instruction to start using VaxPress. Note that -i and -o options are mandatory:

vaxpress -i {path_to_input.fa} -o {path_to_output_directory} --iterations {n_iterations} -p {n_processes}

Input

Provide a CDS sequence in FASTA format. Alternatively, if you have a protein sequence in FASTA format, use the --protein option.

Number of Iterations

By default, the --iterations option is set to 10. For a comprehensive optimization, it's suggested to use a minimum of 500 iterations. However, the ideal number of iterations can vary based on the input's length, composition, and chosen optimization settings. Note that the optimization process might halt before completing all specified iterations if no improvement is detected over several consecutive cycles.

Multi-Core Support

You can use multiple CPU cores for optimization with the -p or --processes option.

Adjusting the Fitness Scoring Scheme

VaxPress optimizes synonymous codon selections to potentially enhance the fitness of coding sequences for mRNA vaccines. This fitness is derived from a cumulative score of various metrics, including the codon adaptation index, GC ratio, among others. To emphasize or de-emphasize a specific feature, simply adjust its weight. A deeper understanding of the scoring functions' principles is available on the optimization algorithm page.

Setting Weights

To fine-tune the optimization, adjust the weights of individual scoring functions using the --{func}-weight option. Setting a function's weight to 0 effectively disables it.

# Concentrate on the stable secondary structure (more weight to the MFE)
vaxpress -i spike.fa -o result-spike --mfe-weights 10

# Turn off the consideration of repeated sequences
vaxpress -i spike.fa -o result-spike --repeats-weight 0

Custom Scoring Functions

VaxPress allows users to add their custom scoring functions. This feature enables a more targeted optimization process by integrating new sequence attributes of interest. For detailed instructions, please refer to the Adding a scoring function page.

Using LinearDesign for Optimization Initialization

LinearDesign (Zhang et al., 2023) offers ultra-fast optimization, focusing on near-optimal MFE and CAI values. By using the --lineardesign option, VaxPress invokes LinearDesign internally then begins its optimization with a sequence already refined by LinearDesign. Subsequent VaxPress optimizations further improves the sequences for features like secondary structures near the start codon, uridine count, in-cell stability, tandem repeats, and local GC content.

To utilize the LinearDesign integration, provide the path to the installed directory of LinearDesign using the --lineardesign-dir option. This option can be omitted in subsequent uses. The --lineardesign option also needs a LAMBDA parameter, which influences the balance between MFE and CAI. Values between 0.5 and 4 are usually suitable starting points. For insights into the LAMBDA value's implications, consult Zhang et al. (2023).

Note that sequences straight from LinearDesign often have suboptimal structures around the start codon. Under the high mutation rate at the beginning, this causes the main sequence body to lose its optimal MFE structure. The -—conservative-start option tackles this by focusing on the start codon region before optimizing the rest. Also, given that LinearDesign's outputs are already quite optimal, the --initial-mutation-rate can be reduced to 0.01. This ensures efficient optimization as there's a minimal likelihood that a better mutation would emerge with a higher mutation rate.

# Running VaxPress with LinearDesign
vaxpress -i spike.fa -o results-spike --processes 36 \
         --iterations 500 --lineardesign 1.0 \
         --lineardesign-dir /path/to/LinearDesign \
         --conservative-start 10 --initial-mutation-rate 0.01

Output

Once you've run VaxPress, the specified output directory will contain the following five files:

• report.html: A summary report detailing the result and optimization process.
• best-sequence.fasta: The refined coding sequence.
• checkpoints.tsv: The best sequences and the evaluation results at each iteration.
• log.txt: Contains the logs that were displayed in the console.
• parameters.json: Contains the parameters employed for the optimization. This file can be feeded to VaxPress with the --preset option to duplicate the set-up for other sequence.

Citing VaxPress

If you employed our software in your research, please kindly reference our publication:

Ju, Ku, and Chang (2023) Title. Journal. Volume.

License

VaxPress is distributed under the terms of the MIT License.

LinearFold and LinearDesign are licensed for non-commercial use only. If considering commercial use, be cautious about using options such as --lineardesign and --folding-engine linearfold.