GibsonAssemblyManager.php
Gibson assembly junction analysis and primer design Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 7 October 2026
Table of Contents
Classes
- GibsonAssemblyManager
- checkJunction() deliberately does NOT reuse the alignment engine (Domain/Alignment, including its own semi-global/overlap aligner) : Gibson's exonuclease chew-back and annealing need the two fragments' homology arm to be essentially IDENTICAL, not merely "well aligned" under some scoring scheme that would tolerate mismatches or gaps a real reaction would not anneal through. An anchored exact-match search - does upstream's very last k bases equal downstream's very first k bases, for the longest k in range - is both the scientifically appropriate check here and simpler than configuring an aligner strictly enough to approximate one.