OrfFinder.php
Finds open reading frames across all six reading frames of a DNA sequence Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 2 October 2026
Table of Contents
Classes
- OrfFinder
- Migrated from biotools' Service/DnaToProteinManager.php::findORF(), which was not actually a coordinate-returning ORF finder : it translated up to six frames into peptide strings and then highlighted the coding stretches (uppercasing a "*"-delimited segment long enough, optionally trimmed to its first Met) purely for display. That highlighting behavior stays a presentational concern of biotools. This class reuses the same core idea - the longest ORF in each stop-delimited segment starts at that segment's first Met - but implements it as a proper library service that returns real OpenReadingFrame coordinates, via SequenceInterface::translateCodon() (the project's own already-wired standard genetic code) rather than biotools' separate TripletApiAdapter/ TripletSpecieApiAdapter machinery, the same reuse CodonAdaptationIndexCalculator already makes.