Six-Frame ORF Finder: Codon-Bias Gene Prediction

Genome annotation starts with a deceptively simple question: given a raw stretch of DNA, where are the genes? This simulator renders a real 3D B-DNA double helix and runs the classic first pass of a gene-finding pipeline on it live — scanning all six reading frames for ATG-to-stop open reading frames, scoring every candidate against a real codon-usage bias table via a log-odds statistic, and lighting up the highest-scoring prediction directly on the helix. Adjust GC content, sequence length and the minimum ORF length to see how genome composition and filtering change what looks like a gene versus what is just noise — the same trade-off every annotation pipeline (GLIMMER, Prodigal, GeneMark) has to make on a real genome.