ORF detector (open reading frames)

Finds, across all six reading frames or the forward strand only, every ORF running from an unambiguous start codon to the first unambiguous stop codon in the same frame. For each: frame, positions on the forward strand, length in nucleotides and amino acids, DNA and protein sequences, and whether it ends at a stop or remains open at the end of the sequence.

In frame +1, the first ATG (position 1) opens an ORF closed by the first TAA (positions 16–18); the second ATG (position 10) opens a shorter, nested one ending at the same stop. A third ATG (position 25) opens a new ORF that ends at the final TAA.

Start codon

codon that initiates translation, ATG (methionine) by default. GTG and TTG, documented alternative starts in prokaryotes, are available as an option.

Stop codon

codon (TAA, TAG or TGA) that ends translation and marks the end of an ORF.

Open ORF

an ORF with no stop codon before the end of the entered sequence; it may continue beyond it.

Nested ORFs

several start codons in the same frame upstream of the same stop codon each open an ORF. All are reported.

Indeterminate ambiguous codon

a codon containing an IUPAC base (N, R, Y…) whose possible readings do not agree on start or stop status. It is not used as an ORF boundary.

The search is purely sequential. Promoters, ribosome binding sites, splicing, codon usage bias and evidence of expression are not examined; in eukaryotes, introns can interrupt a gene. An ORF found is a candidate, not proof of a functional gene. On a long sequence, many short ORFs arise by chance, hence the minimum length filter applied by default.

A reading frame splits the sequence into consecutive codons from a starting point: three frames per strand, six in total. An ORF (open reading frame) begins at a start codon (ATG by default) and ends at the next stop codon in the same frame, or at the end of the sequence.