CircularRestrictionDigestManager.php
Computes restriction enzyme cuts and fragments on a circular Plasmid Freely inspired by BioPHP's project biophp.org Created 24 September 2026 Last modified 8 October 2026
Table of Contents
Classes
- CircularRestrictionDigestManager
- The upper/lower cleavage position convention is locked by RestrictionEnzymeCatalog's fixtures and verified against known biology : cleavagePositionUpper is the offset, from the start of a match, of the upper-strand cut ; cleavagePositionLower is that same offset for the lower strand, expressed relative to the upper one (RestrictionEnzymeDTO's own wording). A positive relative offset produces a 5' overhang, a negative one a 3' overhang, zero a blunt end - checked here against EcoRI (5', offset +4, overhang "AATT"), AatII (3', offset -4, overhang "ACGT") and AatI (blunt, offset 0).