How to Use the ORF Finder
Step 1: Enter your DNA sequence in the input box above.
Step 2: Set the minimum ORF length in base pairs. The default is 100 bp — the widely accepted literature threshold to distinguish real ORFs from random ATG-stop combinations (which occur frequently by chance in sequences shorter than 100 bp). Reduce to 9 bp only for short test sequences; increase to 300+ bp for eukaryotic gene searches.
Step 3: Select which reading frames to search — all 6 frames, forward only, or reverse only.
Step 4: Click Find ORFs. Each found ORF shows its position, length, frame, and sequence with start and stop codons highlighted.
What is an Open Reading Frame?
An Open Reading Frame (ORF) is a continuous stretch of codons that begins with a start codon (ATG) and ends with a stop codon (TAA, TAG, or TGA). ORFs are potential protein-coding regions in a DNA sequence.
1. Scan sequence for ATG (start codon)
2. Continue reading in triplets
3. Stop at TAA, TAG, or TGA (stop codon)
4. Report if length ≥ minimum threshold
// Example sequence:
5' ...NNNN[ATG-AAA-GCA-TGA]NNNNN... 3'
↑start ↑stop
ORF length = 12 bp = 4 codons = 3 amino acids
6 Reading Frames
Any double-stranded DNA sequence has 6 possible reading frames — 3 on the forward strand (starting at positions 1, 2, and 3) and 3 on the reverse complement strand. Real genes can be on either strand in any frame, which is why searching all 6 frames is important.
Minimum ORF Length
Setting a minimum ORF length helps filter out short random ORFs that appear by chance. For finding real protein-coding genes in genomic DNA, a minimum of 100-300 bp is recommended. For short sequences or teaching purposes, 30 bp is a good starting point.