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.

Contents

• Installation
  • Installing VaxPress using Pip
  • Installing VaxPress using Conda
  • Running VaxPress via Singularity
  • Installing LinearDesign
• A Tour Through VaxPress
  • Step 1. Downloading a Sequence
  • Step 2. Evaluating the Given Sequence
  • Step 3. Running VaxPress Optimization
• Usage
  • Input File (-i)
  • Number of Iterations (--iterations)
  • Multi-Core Support (-p)
  • Adjusting the Fitness Scoring Scheme
  • Using LinearDesign for Optimization Initialization
  • Output (-o)
• Command Line Options
  • Input/Output and Execution Options
  • Optimization Options
  • LinearDesign-related Options
  • Options Related to Fitness Functions
• How VaxPress Works
  • Optimization
  • Objective Function
  • Adaptive Decrement of Mutation Rate
• Scoring Functions
  • RNA Folding
  • Codon Usage
  • Other Activity Factors
  • Production Factors
  • References
• User Guides
  • Using LinearDesign for Optimization Initialization
  • Tuning Optimization Parameters
  • Using preset values
  • Modifying the default configuration
  • Adding a custom scoring function
  • References
• Troubleshooting
  • iCodon option is missing
• Licenses
  • VaxPress
  • LinearFold

Indices and tables

VaxPress Documentation Index

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