How it works:

• Analyzes your DNA sequence for potential silent mutations
• Maintains the original amino acid sequence
• Introduces restriction enzyme recognition sites
• Screens against enzymes not already present in your sequence

Parameters:

• Cut Position: Desired location for the new restriction site (1-based index)
• Tolerance: How far from the cut position the site can be placed
• Window Size: Number of codons to consider for mutations
• Max Changes: Maximum number of codon changes allowed

Algorithmic Codon Optimization (Optional):

When enabled, variants are scored using the following metrics:

• CAI (Codon Adaptation Index): 0-1 score measuring codon usage optimization for your host organism. Higher is better.
• Rare Codon Penalty: Penalizes sequences with clusters of rare codons that slow translation
• mRNA Structure Penalty: Penalizes overly stable secondary structures using minimum free energy (ΔG) calculations
• Mutation Penalty: Prefers conservative edits with fewer codon changes
• Restriction Bonus: Bonus for successfully introducing desired restriction site

P-Score = w₁·CAI - w₂·RarePenalty - w₃·StructurePenalty - w₄·MutationPenalty + w₅·RestrictionBonus

Why Use Algorithmic Scoring?

• Transparent, reproducible results based on published bioinformatics metrics
• No AI black box - every component is scientifically justified
• Publishable methodology
• Host-specific optimization (E. coli, Human, etc.)