Optimize a DNA coding sequence or reverse-translate protein for a selected expression host. Compare synonymous codon changes, GC content, host codon usage and remaining unwanted motifs.
Use Download format in the results to save optimized DNA FASTA, protein FASTA or the codon-usage TSV table.
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
Tool mode.
Expression host.
Protein sequence or DNA CDS.
Optional Settings
Tool mode
Use Protein to DNA if you start with protein. Use Optimize DNA CDS for a coding DNA sequence already grouped into complete codons.
Expression host
Choose the organism where you plan to express the protein.
Optimization region (optional)
Enter a 1-based, inclusive range such as 4-300. Start at a codon's first base (1, 4, 7...) and end at its third base (3, 6, 9...). Bases outside the range stay unchanged. Leave blank for the full CDS.
Minimum / maximum GC%
Set a desired whole-CDS GC range. These are optimization targets, not guaranteed limits; inspect final GC% and warnings.
Avoid restriction sites or motifs
Select enzyme names from search suggestions, or enter DNA motifs, separated by commas. Review remaining motif counts; avoidance can conflict with coding constraints.
Upload sequence file (optional)
Use this instead of pasting sequence text.
How To Use
Choose tool mode.
Choose the host.
Paste or upload the protein or DNA sequence.
Check the detected input notice; the tool can switch modes when the input clearly looks like protein, DNA, or GenBank DNA.
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 compares original and optimized GC%, CAI-like host adaptation score, low-usage codons, changed codons, and remaining avoided motifs.
The host-adaptation score describes how closely codon choices follow the selected host's stored frequencies. Low-usage codons are uncommon in that table. A higher score does not guarantee higher expression. Check the protein sequence, final GC% and remaining unwanted motifs.
The result identifies the host taxon, source and CDS count. The codon table shows synonymous choices and changes made.
Copy optimized DNA or protein FASTA, or send the optimized DNA directly to Primer Designer.
Accepted Input Formats
Protein sequence or protein FASTA using one-letter amino acid codes. X becomes NNN; B and Z are resolved to one of their possible amino acids, with a warning. Resolve uncertain residues before ordering DNA.
DNA CDS, DNA FASTA, or GenBank text with an ORIGIN section in Optimize DNA CDS mode.
DNA CDS must use complete codons under the standard genetic code. U is converted to T. Codons containing IUPAC ambiguity bases are left unchanged and excluded from host-adaptation scoring. Supply a coding sequence, not a genomic region containing introns.
Multiple FASTA records are concatenated. Process unrelated records separately to avoid artificial junctions.
.dna / SnapGene binary files are not supported. Export DNA as FASTA or GenBank.
Assumptions And Limitations
Synonymous codon changes preserve the encoded protein, but higher expression is not assured. The optimizer does not model mRNA folding or protein folding.
Avoiding motifs may not always be possible with all other constraints.
The CAI-like score estimates codon-usage adaptation; it is not a direct prediction of protein expression.
Host tables use a versioned FDA HIVE-CoCoPUTs snapshot. The public service is labelled September 2021 and its README identifies RefSeq 99 / GenBank 238.0; retrieval in September 2026 does not make it a 2026 genome dataset. Results and exports identify the taxon, source and CDS count. RefSeq genomic data are preferred; Nicotiana benthamiana uses a smaller GenBank fallback table.
Cell-line host entries, including CHO, HEK-293, NS0, BHK-21, PER.C6, Sf9 and High Five, use organism-level codon usage rather than cell-line-specific expression data.
K. phaffii and O. polymorpha use their own taxa, not the legacy K. pastoris or Pichia angusta tables. Pf-5 is listed as Pseudomonas protegens, with its former P. fluorescens name retained.
Supply the CDS in coding-strand order. If it crosses base 1 in a circular sequence, extract and join its parts in the correct order before analysis; do not submit the whole plasmid as a CDS.
Check the final sequence against your vector, synthesis provider, and host system.
The browser tool accepts files smaller than 2 MB, DNA up to 250,000 bases, and protein up to 100,000 amino acids.
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 this result with other tools
Direct transfer: after optimization, use Send optimized DNA to Primer Designer to send the optimized DNA to Primer Designer. Confirm the imported sequence and choose the amplicon region, primer length or target Tm, then design. Host settings, codon scores and the input protein are not transferred.
Manual follow-up: copy the optimized DNA into Restriction Site Analyzer to review recognition sites, or into ORF / Protein Translator to translate it and compare the protein. Copy it as an insert into an assembly designer when joining it to a vector. Review any unknown-codon output first: Primer Designer requires unambiguous A/C/G/T DNA.
Correcting highlighted input
When the main action rejects pasted sequence text, unsupported characters are highlighted in the field and the error message explains the problem. Correct the marked characters using the alphabet allowed by this tool, then run it again. The highlights update as you edit. A malformed FASTA or GenBank record may require a structural correction even when no individual character is marked.
Use note: These tools are for research and educational planning. Check important calculations and sequence designs before ordering reagents or running experiments.