Does optimization change the protein?

No. Codon substitutions are synonymous, so the encoded protein is preserved while the underlying codons change.

What happens when constraints conflict?

The solver reports the constraints it could not satisfy rather than returning a sequence that quietly violates one.

Design · experimental

Codon Optimization

Rewrite a coding sequence for expression in a chosen host while holding the constraints that matter: forbidden restriction sites, GC window, homopolymer limits, and the encoded protein. The solver reports which constraints it satisfied and which it could not, instead of silently returning a sequence that breaks one.

Open Codon Optimization Open the Codon usage sample

Thirteen real CDSs — yeast ADH1, ten mammalian expression parts (mTagBFP2 · PuroR ×2 · BSDR · Kozak-ATG · linker · IgK leader · L7Ae), the rare-codon-loaded ccdB cassette, pBR322 for its reverse-strand bla and human EMX1 for a three-exon spliced CDS: compare CAI, GC and rare codons across hosts, and optimize a gene that runs the other way

What it does

01Expression design: one sequence per published strategy, compared side by side
02Codon optimization against a selected host codon usage table
03Hard constraints, including forbidden enzyme sites, GC window and homopolymer limits
04Protein-preserving optimization, so the translation is unchanged
05Region-scoped optimization, for a single CDS inside a larger construct
06A report naming every constraint that could not be satisfied
07A saved comparison carrying every design, its scores and where each number came from

What it runs on

The optimizer is a port of DnaChisel, golden-validated against the Python implementation. The panel runs on @ports/codon, @ports/enzymes, @ports/expression-postures, @ports/optimize, @ports/repofetch, @ports/splice, @ports/workflow.

Everything runs client-side. Files are parsed in the browser and projects are saved on this machine, so an unpublished sequence is never uploaded.

Questions

Does optimization change the protein?: No. Codon substitutions are synonymous, so the encoded protein is preserved while the underlying codons change.
What happens when constraints conflict?: The solver reports the constraints it could not satisfy rather than returning a sequence that quietly violates one.

Also searched as

codon optimization tool · codon optimize gene online · DNA optimization for expression · remove restriction sites from gene · GC content optimization · DnaChisel online · synthesis-ready sequence design · IDT codon optimization alternative · GeneArt codon optimization alternative · optimize a gene for E. coli expression · optimize a gene for yeast expression · codon harmonization tool · compare codon optimization strategies · codon optimization vs harmonization · mRNA folding energy at the start codon · gene synthesis design tool · avoid unwanted restriction sites in a synthetic gene