ORF finder: open reading frames

Worked example

• The first 1,500 bases of the E. coli lac operon (J01636.1) with the bacterial code (table 11), ATG to stop, 75 nt or longer: 5 ORFs listed, 6 nested and hidden, 1 with no stop before the sequence ends.
• The longest, 202 to 1161 on the + strand, is 960 nt and 319 residues: the lacI repressor.
• Turning on the table's alternative initiation codons (GTG, TTG and the others in table 11) adds ORFs that start without ATG; the setting is on the card.

Method

From a permitted start codon to the next in-frame stop; coding length ≥ the minimum; an ORF inside another is nested

• Open reading frames. NCBI ORFfinder conventions as the CSO set them on 6 October 2026: ATG (or the table's initiation codons) to the table's stop, 75 nt counted to the codon before the stop, nested ORFs hidden, ORFs without a stop listed apart.Checked field by field against an independent scan cross-checked with Biopython 1.88 and NCBI ORFfinder 0.4.3 on 18 cases (6 October 2026).
• Translation with NCBI's genetic code tables. NCBI. The Genetic Codes, gc.prt version 4.6 (last modified 10 June 2020), fetched 2026-10-06. Public domain.Checked against Biopython 1.88 exactly on 108 frame translations of three sequences in genetic codes 1, 2 and 11, full length and to the first stop, and on 5 annotated coding sequences (6 October 2026).