A naΓ―ve gene finder reads a genome in all six reading frames β three forward offsets (0, +1, +2) on the given strand, plus the same three offsets on its reverse complement β because a real gene can sit on either strand and start at any of three codon phases.
Within each frame the scanner walks codon by codon. The first ATG it meets opens a candidate open reading frame (ORF); the ORF closes at the next in-frame stop codon (TAA, TAG, TGA). Everything between is a candidate protein-coding stretch.
Not every ORF is a real gene β random DNA throws up plenty by chance. To rank candidates this simulator scores each one with a codon-usage log-odds statistic, comparing how often each codon appears in real coding sequence (an E. coli-derived usage table, per 1000 codons) against how often it would appear by chance given the sequence's own GC content:
S = Ξ£ log2( f_coding(codon_i) / f_background(codon_i) ) for i = 1..L codons
f_background(XYZ) = p(X)Β·p(Y)Β·p(Z), p(G)=p(C)=GC/2, p(A)=p(T)=(1βGC)/2
Real coding regions are biased toward a small set of "preferred" codons for each amino acid (translation is faster/more accurate with abundant tRNAs), so a genuine gene scores well above zero; random ORFs hover near zero or below. The predicted gene shown on the helix is the qualifying ORF (at least the minimum length) with the highest score β exactly the ranking step real annotation pipelines (e.g. GLIMMER, Prodigal) use a Markov codon model for, simplified here to single-codon log-odds.
- GC content β reshapes the background model and the random sequence itself; higher GC favors G/C-rich codons by chance alone, so the scanner has to work harder to tell signal from noise.
- Sequence length / New Random Sequence β regenerates the helix; longer sequences turn up more spurious short ORFs.
- Min. ORF length β the length filter every real annotation pipeline applies first, since short spurious ORFs are common in any random sequence.
- Highlight all qualifying ORFs β shows every frame's candidates at once instead of only the top prediction.