What is an open reading frame (ORF)?

An ORF is a continuous stretch of codons beginning with a start codon (ATG) and ending with a stop codon (TAA, TAG, or TGA) in the same reading frame, with no intervening stop codons. It represents a potential protein-coding sequence.

How many reading frames are searched?

Six reading frames are searched: three on the forward strand (starting at positions 0, 1, and 2) and three on the reverse complement strand. This ensures every possible ORF is found regardless of orientation.

Can I paste RNA sequences?

Yes. The tool automatically converts U to T before analysis, so RNA sequences (using U) work exactly the same as DNA sequences (using T).

What does the minimum length filter do?

It hides ORFs shorter than the specified number of nucleotides (including start and stop codons). A common threshold is 100 nt (about 33 amino acids) to filter out random short ORFs that are unlikely to encode functional proteins.

What amino acid symbols are used in the translation?

Standard single-letter IUPAC amino acid codes are used (e.g., M for methionine, * for stop). The genetic code applied is the standard (NCBI translation table 1).

Does the tool handle degenerate bases?

Degenerate IUPAC bases (N, R, Y, etc.) are treated as unknown. Codons containing degenerate bases are translated as "X" (unknown amino acid).

Open Reading Frame (ORF) Finder

Paste a DNA or RNA sequence to find all open reading frames across all 6 reading frames, with start/stop positions and translated protein sequences.

DNA / RNA Sequence

0 nt

Min ORF length (nt)

Strand

Enter a sequence and click "Find ORFs"

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Total ORFs

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Longest (nt)

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Frames hit

#	Frame	Start	Stop	Length	Protein (aa)

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Summary

The ORF Finder scans a DNA or RNA sequence across all six reading frames — three on the forward strand and three on the reverse complement strand — to locate every open reading frame. Each ORF is defined as a sequence beginning with a start codon (ATG) and ending with a stop codon (TAA, TAG, or TGA). Results include the frame, strand direction, start and stop positions, length in nucleotides, and the translated amino acid sequence.

How it works

Paste or type your DNA or RNA sequence into the input box.
Choose the minimum ORF length filter to hide short noise ORFs.
Click "Find ORFs" to scan all 6 reading frames.
Results appear sorted by length — longest ORF first.
Click any ORF row to highlight its nucleotide sequence and copy the protein translation.

Use cases

Identify candidate protein-coding regions in a newly sequenced gene.
Verify that a cloned insert contains the expected reading frame.
Find all potential ORFs in a viral genome segment.
Check for alternative ORFs in overlapping reading frames.
Translate a known CDS to its amino acid sequence.
Confirm stop codon placement in expression constructs.

Frequently Asked Questions

Last updated: 2026-09-30 · Reviewed by Nham Vu