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Six-frame translation

All three forward and three reverse frames at once. The frame with the longest open stretch is marked.

Six frames

What a six-frame translation shows

DNA is read in codons of three bases, so a strand can be translated starting at its first, second or third base, and the complementary strand adds three more starting points. Those are the six reading frames. A six-frame translation writes out the protein each of them would give. Only one frame is the real one for any gene, and the tool helps you spot it: it marks the longest stretch without a stop codon in every frame and highlights the frame with the longest stretch overall. To translate a single chosen frame, use theDNA to protein translator; to list every open reading frame with coordinates, use the ORF finder.

How to read the output

Frames +1, +2, +3 read the sequence as pasted from its first, second and third base. Frames −1, −2, −3 read the reverse complement the same way, so −1 starts at the last base of your sequence. Stop codons are shown as a red*, methionines in blue, and the longest open stretch in each frame is shaded. The header of each frame gives its length in amino acids, its number of stops and the length of that stretch. In random sequence a stop appears about every twenty codons, so a frame with a shaded run of fifty or more residues is almost certainly the coding frame.

When you need all six frames

  • Unannotated sequence from a sequencing read, a PCR product or a metagenome, where the strand and the phase are unknown.
  • Checking a construct. After cloning, confirm that the insert sits in frame with the tag or promoter by looking for the uninterrupted frame.
  • Frameshift mutations. A frameshift moves the protein from one frame into the next; comparing frames shows where the run of sense ends and the stops begin.
  • Searching a database with DNA. Tools such as BLASTX translate the query in all six frames for the same reason; this page lets you see what they see.

Genetic codes and ambiguous bases

The standard code is the default. Mitochondrial and other NCBI variant codes are available from the menu, using the same table numbers as GenBank and BLAST. IUPAC ambiguity codes are resolved codon by codon: a codon whose possible readings all give the same amino acid is translated, and one whose readings disagree is written as X. U is read as T. Multi-record FASTA is translated record by record, six frames each.

Frequently asked questions

What are the six reading frames?

Three on the forward strand, starting at base 1, 2 or 3, and three on the reverse complement strand read in its own 5′ to 3′ direction. Every stretch of double-stranded DNA can in principle be read in all six, but a real gene uses only one.

How do I tell which frame is the coding frame?

Look for the frame with a long run of amino acids with no stop codon. Random sequence hits a stop about every 20 codons, so a stretch of 50 or more residues without one is almost always a real coding region. The tool reports the longest open stretch in each frame and marks the best.

What do the frame names +1, +2, +3, −1, −2, −3 mean?

The sign is the strand: + for the sequence as pasted, − for its reverse complement. The number is the starting base, so +2 reads the forward strand from its second base. −1 reads the reverse complement from its first base, which is the last base of the forward strand.

Why is the same protein not visible in the reverse frames?

Because the reverse frames read the other strand, which encodes different codons. A gene on the forward strand appears only in one forward frame; a gene on the reverse strand appears only in one reverse frame.

Can I use a mitochondrial genetic code?

Yes. The genetic code menu offers the standard code and the common NCBI variants, including vertebrate and invertebrate mitochondrial codes, and all six frames are translated with the code you choose.