OpenReadingFrame.php
Immutable value object describing one open reading frame found in a DNA sequence Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 2 October 2026
Table of Contents
Classes
- OpenReadingFrame
- frame follows the standard six-frame convention : +1/+2/+3 for the forward strand (the reading frame's zero-based offset plus one), -1/-2/-3 for the reverse strand (the same, on the reverse complement). start/end are always given as ascending 1-based inclusive positions in the ORIGINAL, forward-strand sequence - even for a reverse-strand ORF, the same convention GenBank's own complement(start..end) location uses, so a negative frame's coordinates stay directly comparable to a positive one's. end includes the stop codon's three bases when hasStopCodon() is true ; getPeptide() itself never includes the "*" stop symbol.