ORF Finder
Find the open reading frames in a DNA sequence: all six frames, a minimum length you choose, starting at ATG, at any start codon of the genetic code, or straight after the last stop. Each ORF shows its position, length and protein, on the sequence and in a table.
Sequence tool
Find open reading frames
Bare letters, a FASTA record or a GenBank record. Numbers and spaces from a listing are ignored.
Stop codon included. NCBI's ORFfinder starts at 75.
Paste a DNA sequence to find its open reading frames.
Worked example
Human insulin mRNA (NM_000207.3, 465 nt)
- 01six frames, ATG starts, at least 75 nt
- 02frame +3: ATG at 60 to the TAG ending at 392: 333 nt, 110 aa
- 03frame −3: 355 → 206, 150 nt, 49 aa; nothing else reaches 75 nt
Two ORFs. The 333-nt one at 60–392 is the insulin coding sequence, and its protein is preproinsulin; the 150-nt one on the other strand is chance.
How it works
The reasoning behind it
An open reading frame is a stretch of codons with no stop codon in it, read in one frame. A gene's coding sequence is an ORF that begins with a start codon, so the tool walks each of the six frames codon by codon, notes the first start codon it meets, and reports the stretch when it reaches a stop.
The six frames are the three ways of reading the pasted strand and the three of reading its reverse complement. An ORF on the reverse strand is reported with its start and end as the forward strand numbers them, so the start is the higher number.
Chance makes short ORFs everywhere: three of the 64 codons are stops, so a random frame stays open for about 21 codons on average. A minimum length filters them, and the longest ORF in an mRNA or a cloned insert is nearly always the gene.
Questions
Frequently asked
What is an open reading frame?
A run of codons in one reading frame with no stop codon, usually counted from a start codon to the next stop. It is the stretch a ribosome could translate, so a long one is the first sign of a gene.
Why does NCBI's ORFfinder give a different count?
The settings differ. ORFfinder's default is also 75 nt and ATG only, but it can list nested ORFs that start at a later ATG inside a longer one, and it has options for the start codons this tool doesn't offer. With the same settings the long ORFs agree.
Which ORF is the gene?
In an mRNA or a cDNA, the longest one, nearly always on the plus strand. In a cloned insert it is the one in the frame the vector expects. For a genomic sequence from a eukaryote, none of them may be: introns break the coding sequence into pieces.
What do the minus frames mean?
They read the other strand. The ORF's start and end are given as the forward strand counts them, so a minus-strand ORF has its start at the higher number and runs leftwards. Its protein is translated from the reverse complement.
More Calculators
Each one shows its formula and a worked example, so you can check the answer and learn the method.
DNA to Protein Translation
Translate DNA or RNA into protein in any of the six frames, with the standard or a mitochondrial or bacterial code, and get the protein's mass and pI.
Open the toolReverse Complement
The reverse complement, complement or reverse of a DNA or RNA sequence, or DNA written as RNA, from bare letters or FASTA.
Open the toolRestriction Map
Where 109 common enzymes cut a sequence or plasmid, the fragments a digest gives on a virtual gel, and the enzymes that cut once or not at all.
Open the toolPractice the theory with free quizzes in Molecular Biology, Genetics, Bioinformatics, Biotechnology and Microbiology.