ORF Finder and Protein Translator Help

Useful Checks

• Use the checked coding region with Primer Designer when you need PCR primers around an ORF or insert.
• Use ORF results with Codon Optimizer when moving from a DNA coding sequence to expression planning.

How To Use

1. Choose ORF finder or Quick translate.
2. Paste or upload the sequence.
3. Adjust frame, region, or ORF length only if needed.
4. Click Analyze sequence in ORF finder mode or Quick translate in Quick translate mode.

Understanding The Results

• Frame summaries show translations and stop codons.
• The ORF table shows position, strand, frame, length, and sequence actions.
• Show sequence opens a row's sequence details; Hide sequence closes them. Copy DNA returns the coding strand 5′ to 3′; Copy protein returns its translation.
• ORF proteins FASTA contains the listed proteins. Translations FASTA instead contains the selected frame translations, rather than only the listed ORFs.
• ORF DNA FASTA gives the coding strand written 5' to 3', including the terminal stop codon when present. ORF protein output excludes that stop codon.
• Quick DNA results provide the selected frame or all six translated frames.
• Quick protein results include one possible coding DNA and a degenerate IUPAC DNA library. The library can also encode unintended amino acids or stops, especially for leucine, serine and arginine. Review the warning; use the possible coding DNA when you need one sequence encoding the input.

Accepted Input Formats

• Raw DNA, DNA FASTA, or GenBank text with an ORIGIN section for ORF finder and Quick translate DNA input.
• Raw protein or protein FASTA for Quick translate protein input.
• FASTA headers are ignored. Multiple records are concatenated, so process unrelated records separately to avoid artificial junctions.
• U in DNA input is converted to T.
• Ambiguous codons may translate as X.
• .dna / SnapGene binary files are not supported. Export as FASTA or GenBank.

Assumptions And Limitations

• The current ORF finder uses the standard genetic code and exact ATG starts with TAA, TAG, or TGA stops. Ambiguous start or stop codons are not treated as exact starts or stops.
• Protein-to-DNA reverse translation is not unique and is not host-specific codon optimization.
• For an ORF crossing a circular sequence's base 1, rotate the sequence text so the ORF is contiguous before analysis. No physical linearization is needed.
• A long ORF alone establishes neither a gene annotation nor protein expression. Use organism-appropriate translation, sequence similarity and experimental evidence to assess function.
• The browser tool accepts files smaller than 2 MB, DNA up to 250,000 bases, and protein up to 100,000 amino acids.

Example

When The Expected ORF Is Missing

• Choose all six frames and the full sequence first. Lower Minimum ORF length if the expected protein is short, and raise Max ORFs shown if the result list is capped.
• The finder requires an exact ATG start and uses the standard genetic code. A coding sequence with an alternative start or genetic code may not appear as expected.
• Enable Include open-ended ORFs when the sequence lacks a terminal stop. This does not remove the ATG-start requirement.
• Check for sequencing errors, introns and internal stops. Quick translate can inspect a selected frame without requiring an ATG start; it does not splice out introns or repair the sequence.

Use this result with other tools

There is no direct send-to-tool button. Copy the coding-strand DNA of a chosen ORF into Primer Designer to design primers for that region, or into Codon Optimizer to adjust synonymous codons. You can also copy the translated protein into Codon Optimizer’s protein-input mode when you want it to propose a coding sequence.

For a reverse-strand ORF, use the ORF’s coding-strand sequence in 5′ to 3′ orientation. Coordinates in an extracted ORF are relative to that extracted sequence, not the original full template. If you need the flanking DNA too, keep the original template and enter its intended region in Primer Designer.

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.