Use this to redesign a coding sequence with synonymous codons for a selected expression host. It can start from a protein sequence or DNA CDS, but optimized codons are not a guarantee that the protein will express.
Useful Checks
Use ORF and Protein Translator to verify that the optimized DNA still translates to the expected protein sequence.
After optimization, send the optimized DNA to Primer Designer to plan PCR primers around the edited coding sequence.
Minimum Inputs Needed
Input mode.
Expression host.
Protein sequence or DNA CDS.
Optional Settings
Input mode
Use Protein -> optimized DNA if you start with protein. Use DNA CDS -> optimized synonymous DNA if you already have a coding sequence.
Expression host
Choose the organism where you plan to express the protein.
Optimization region (optional)
Optimize only part of a DNA CDS. Leave blank to optimize the full CDS.
Minimum / maximum GC%
Use this if you want the optimized DNA within a GC range.
Avoid restriction sites or motifs
Enter enzyme names or DNA motifs you want to reduce or remove.
Upload sequence file (optional)
Use this instead of pasting sequence text.
How To Use
Choose input mode.
Choose the host.
Paste or upload the protein or DNA sequence.
Set GC range or avoided motifs only if needed.
Click Optimize sequence.
Understanding The Results
Optimized DNA FASTA gives the redesigned coding sequence.
Protein FASTA helps confirm the intended protein sequence.
The summary shows GC%, codon-use score, low-use codons, and avoided-site results.
The codon table shows which codons were used.
Accepted Input Formats
Protein sequence or protein FASTA.
DNA CDS or DNA FASTA.
DNA CDS should be in-frame and use complete codons.
Assumptions And Limitations
Codon optimization is a design aid, not an expression guarantee.
Avoiding motifs may not always be possible with all other constraints.
Check the final sequence against your vector, synthesis provider, and host system.
Example
Paste a protein sequence, choose E. coli, keep the default GC range, add EcoRI or BamHI to avoided motifs if needed, and copy the optimized DNA FASTA.
Use note: These tools are for research and educational planning. Check important calculations and sequence designs before ordering reagents or running experiments.