How to use it
- Paste the sequence. Line breaks, numbers and FASTA headers are fine.
- Pick the minimum length; 75 nt is a common default for genes, shorter values find small peptides.
- Choose ATG starts or any codon after a stop, and one or both strands.
- Read the list: frame, start and end positions, lengths, and the protein. Use the copy button next to a protein to take it to a BLAST search or another tool.
How it works
For each frame the finder steps through the codons. In ATG mode an ORF opens at the first ATG after a stop; in “any codon” mode at the first codon after a stop or at the start of the sequence. It closes at the next in-frame stop. The minus strand is read on the reverse complement and its coordinates are converted back to the entered strand.
Worked example
ATGAAATAG reads ATG AAA TAG in frame +1: one ORF from base 1 to 9, 9 nt, protein MK. Its reverse complement, CTATTTCAT, has the same ORF in frame −1, reported as 9–1.
The default sequence encodes a variant of green fluorescent protein (GFP), with short flanks. With a 75 nt minimum the finder lists 11 ORFs; the longest, frame +3 from base 9 to 728, is 720 nt and encodes the 239-amino-acid protein that starts MASKGEELFTG.
Tips
- The longest is not always the gene. In random-looking sequence, short ORFs appear by chance on every frame; real genes in bacteria are usually hundreds of codons long.
- Check the strand. Genes on the minus strand show up only with both strands selected.
- Introns. Eukaryotic genomic DNA is interrupted by introns, so an ORF finder works best on mRNA or cDNA sequences.