ORF detector (open reading frames)
ATG AAA CTG ATG CAT TAA CCC GGG ATG TTT TAA
Paste a DNA sequence: the tool searches, across all six reading frames (or the forward strand only), from every certain start codon to the nearest certain stop codon, and reports for each ORF its orientation, its frame, its start and end positions on the forward strand, its length in nucleotides and amino acids, its DNA sequence, its protein sequence, and whether it ends with a stop codon or stays open at the end of the sequence. A codon containing an ambiguous IUPAC base is never treated as a start or a stop until every one of its possible realizations agrees on that status.
Scientific dossier
What the tool computes, what it assumes, where it stops being valid, and where its data comes from.
Method & formulasATG AAA CTG ATG CAT TAA CCC GGG ATG TTT TAA
ATG AAA CTG ATG CAT TAA CCC GGG ATG TTT TAA
On this sequence, frame +1: the first ATG (position 1) opens an ORF ending at the first TAA (position 16-18), and the second ATG (position 10) opens its own, shorter ORF up to the same stop. Two nested ORFs, both reported. A third ATG further on (position 25) opens a new ORF up to the final TAA.
- Start codon
- · codon that initiates translation, ATG (methionine) by default; GTG and TTG are documented alternative starts in prokaryotes, enabled explicitly.
- Stop codon
- · codon (TAA, TAG or TGA) that ends translation, marks the end of an ORF.
- Open ORF
- · an ORF for which no stop codon was found before the end of the entered sequence: it could potentially continue beyond what was provided.
- Nested ORFs
- · several start codons within the same frame, before the same stop codon, each produce their own valid ORF: this tool reports all of them, not just the longest.
- Indeterminate ambiguous codon
- · a codon containing an IUPAC base (N, R, Y...) whose possible realizations don't all agree on start/stop status: it is never treated as an ORF boundary, so as to never invent a certainty the sequence doesn't support.
Validity domainThis detection is purely sequential: it spots a start.
This detection is purely sequential: it spots a start.stop pattern, nothing more. It checks neither a promoter, nor a ribosome binding site. Nor actual expression evidence, nor splicing (in eukaryotes, a gene can be interrupted by introns that no analysis of the genomic sequence alone can detect). A detected ORF is therefore a candidate worth examining, never proof that a functional gene exists there. On a long sequence, many short ORFs appear by pure statistical chance, which is why a minimum length filter is applied by default.
Reading frame vs. ORF: two distinct notionsA reading frame is simply a way of splitting the sequence into consecutive codons from a starting point (three choices per strand, six in total).
A reading frame is simply a way of splitting the sequence into consecutive codons from a starting point (three choices per strand, six in total). An ORF (open reading frame) is a specific span within one frame: it begins at a start codon (ATG by default) and ends at the first stop codon found afterward in that same frame, or extends to the end of the sequence if no stop is found. A single reading frame may contain zero, one, or several ORFs.