RestrictionCut.php
Immutable value object describing one restriction enzyme cut on a circular plasmid Freely inspired by BioPHP's project biophp.org Created 24 September 2026 Last modified 2 October 2026
Table of Contents
Classes
- RestrictionCut
- All positions are zero-based, consistently with CircularDnaSequence, and already wrapped within [0, plasmid length[. recognitionPosition is where the enzyme's recognition pattern was matched; upperCutPosition and lowerCutPosition are the boundary positions where the upper and lower strands are actually severed, which may differ from recognitionPosition for enzymes cutting outside their own recognition sequence (Type IIb and IIs). reverseStrand tells whether the recognition sequence was found on the plasmid's own reference strand (false) or only detectable as its reverse complement, i.e. the enzyme actually binds the other strand (true) ; upperCutPosition and lowerCutPosition are always expressed in the reference strand's coordinates either way.