Home / Science / Molecular and cell biology / Molecular biology / DNA sequence toolsTool #163

DNA sequence tools: reverse complement, translate in six frames, find open reading frames (ORFs), GC content and codon usage

Paste a DNA or RNA sequence or open a FASTA file. Get the length and GC content, the reverse complement, the protein in any of the six reading frames, every open reading frame above a length you choose drawn on a map, and a codon usage table. Runs in your browser; your sequence never leaves the device.

Keep it one tap away for everyday use.

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  1. Sequence
  2. Complement
  3. Find ORFs
  4. Codon use
Nothing is uploadedWorks offline once open

Sequence

FASTA or plain text, up to 20 MB. The file stays on your device.

Only the first record of a multi-sequence FASTA file is used. Spaces, numbers and line breaks are ignored, IUPAC ambiguity letters (N, R, Y…) are kept, and U is read as T. Up to 5 million bases. The example is a made-up random sequence with two reading frames planted in it.

Summary

Reverse complement

Translation

Standard genetic code. * is a stop codon and X a codon with an ambiguity letter. Frames −1 to −3 read the reverse complement.

Open reading frames

Codon usage

RSCU (relative synonymous codon usage) is how often a codon is used compared with an even share among the codons for the same amino acid: 1 is even, above 1 is preferred.

Codon table
Download

What it does

This page does the everyday jobs people reach for a sequence tool for, without sending the sequence anywhere. Paste a sequence (plain letters or FASTA, DNA or RNA) or open a FASTA or text file, and you get:

  • Summary: length, GC content, base counts and how many open reading frames were found.
  • Reverse complement: the other strand read 5′ to 3′, with ambiguity codes (R, Y, N and so on) complemented correctly. Copy it or download it as FASTA.
  • Translation: the protein in any of the six frames (+1, +2, +3 on the strand you pasted, −1, −2, −3 on the other). Stops show as *; a codon with an ambiguous base shows as X.
  • Open reading frames: every stretch from a start (ATG) to a stop above your minimum length, on one or both strands, on a map of the six frames and in a table you can download as CSV, with the proteins as FASTA.
  • Codon usage: how often each codon is used in the longest ORF, all ORFs, or frame +1 of the whole sequence, with RSCU (relative synonymous codon usage: 1 means a codon is used exactly as often as its synonyms, above 1 means it is preferred).

How to use it

  1. Sequence. Paste it, or open a FASTA or text file (up to 20 MB; sequences up to 5 million bases). With several FASTA records, the first is used. Spaces, numbers and line breaks are ignored; U is read as T. Letters that are not bases are dropped and counted.
  2. Frame. Pick the frame to translate.
  3. ORF settings. Minimum length in amino acids (30 by default; real genes are usually longer than 100). An ORF starts at the first ATG after a stop, or just after a stop (stop to stop) to find every open stretch whatever the start codon. Set Strands to Top strand only to search only the strand you pasted.
  4. Codon usage. Choose which sequence to count.

Positions are 1-based on the strand you pasted, and an ORF’s end includes its stop codon, so a reverse-strand ORF reads from its end back to its start.

Worked example

The example is a made-up 732-base sequence with 362 G and C, so GC is 49.5 %. With a 30 amino acid minimum the tool finds 2 ORFs. The longest is in frame +2, from base 41 to 406: 366 bases, 121 amino acids plus the stop. The second is on the reverse strand in frame −1, from base 457 to 702, 81 amino acids. Both are complete (they start with ATG and end with a stop). Lower the minimum to 10 and short chance ORFs appear, which is why a sensible minimum matters: in random sequence a stop turns up about every 21 codons.

Good to know

  • Only the standard genetic code is used. Mitochondria and some microbes use other codes, so their translations will differ in places.
  • An ORF is a candidate, not a proven gene. Introns, frameshifts and alternative starts are not handled.
  • Everything runs in your browser. Nothing is uploaded or saved.

FAQ

Why does my protein start with M but not end with *? The ORF runs off the end of the sequence without a stop; it is marked incomplete.

What does stop to stop do? It reports open stretches between stops in each frame, which is useful for fragments that may have lost their start codon.

Can it read GenBank files? Not yet. Save the sequence as FASTA first.

Where the numbers come from

  • Standard genetic code (NCBI translation table 1) and the IUPAC nucleotide ambiguity codes: general textbook facts.
  • Reverse complement, six-frame translation, ORF finding and relative synonymous codon usage (RSCU) written by fibub and checked in the tests against Biopython 1.88.
  • The example sequence is random, made up for this page, with two reading frames planted in it. It is not from any real organism.

Standard scientific values, such as constants, atomic weights and melting points, are facts found in every textbook; we name where ours were checked. If you are an author or publisher and want a value, a credit or a table changed or removed, tell us and we will act quickly.

Last updated 2026-11-09.

Change log for DNA sequence tools

  1. Add #163 DNA sequence tools: reverse complement, six-frame translation, ORF finder and codon usage Details on GitHub

Every change to fibub

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