LinearRestrictionDigestManager.php
Computes restriction enzyme cuts and fragments on a linear DNA sequence Freely inspired by BioPHP's project biophp.org Created 9 October 2026 Last modified 9 October 2026
Table of Contents
Classes
- LinearRestrictionDigestManager
- The same geometry as CircularRestrictionDigestManager (see its docblock for the derivation of the two cut positions, on either strand), without the wrapping : a site is searched on both strands but must lie wholly inside the sequence, and a cut is kept only when both its strands are cut inside the sequence. A Type IIs enzyme, which cuts away from its site, therefore loses a site near an end of the sequence - a warning says which. Positions are zero-based junctions : a cut at u leaves u bases on its left. The fragments are the top strand between two distinct upper cuts ; the two ends of the sequence itself are blunt, the only way a bare strand can be taken.