Codon optimization and reverse translation

Use this page when you need to reverse translate protein input or optimize an in-frame coding target in RayCrest MDS while keeping the encoded amino-acid sequence fixed.

Workflow steps

  1. Open the coding sequence or protein input you want to change in the same workspace you use for plasmid editing.
  2. If you are starting from protein input, use Tools > Reverse Translate… to create coding DNA from the amino-acid sequence.
  3. Choose the optimization mode that matches your goal:
  4. Classic for balanced codon optimization
  5. Harmonize for preserving relative codon-usage patterns
  6. Review the codon-change preview and sequence metrics before you keep the result.
  7. Save the optimized sequence, then continue to primer design or map review if you still need to stage downstream work.

Sequence workspace with overlays enabled for coding-sequence design Keep codon work close to construct editing so primer and map review can stay in context.

What this workflow supports

  • Reverse translate raw amino-acid text or one protein FASTA record into coding DNA.
  • Optimize CDS features or other in-frame DNA targets while preserving the amino-acid sequence.
  • Use Classic and Harmonize as the current user-facing optimization modes.
  • Review codon changes, codon or amino-acid context, and sequence metrics in the same workspace used for plasmid editing.

When to use it

  • Starting from a protein sequence and needing a coding-DNA starting point.
  • Starting from an existing CDS or other in-frame DNA target that needs codon changes without changing the protein sequence.
  • Comparing alternative coding-sequence designs in the same local workspace used for plasmids, maps, and primers.

Mode notes

Classic

Classic is the balanced codon-optimization mode for coding-sequence design when improving codon usage is the main goal.

  • Improves Codon Adaptation Index (CAI).
  • Preserves the amino-acid sequence.
  • Maintains codon diversity instead of collapsing onto one codon everywhere.
  • Penalizes avoidable repeats, GC/CpG extremes, and flagged motifs.

Harmonize

Harmonize is the codon-harmonization mode for workflows that preserve relative translation-speed patterns from the source organism while adapting the sequence for the target organism.

  • Compares codon rarity between source and target organisms.
  • Preserves relative codon-usage patterns rather than only preferring the most common codons.
  • Tries to preserve translation pauses that may matter for folding kinetics.

Notes on current scope

  • RayCrest MDS does not currently document direct expression-yield prediction, synthesis-vendor optimization, batch codon optimization, or automatic wet-lab performance claims.
  • Protein input is handled through the dedicated reverse-translate workflow, not as a generic file import path for protein documents.
  • Codon optimization targets must be in-frame DNA and divisible by 3.