CpGIslandFinder.php
Finds CpG islands in a DNA sequence Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 9 October 2026
Table of Contents
Classes
- CpGIslandFinder
- Net-new (present in neither BioPHP nor biotools). Implements the classic Gardiner-Garden & Frommer (1987) criteria : a window qualifies when its GC content and its observed/expected CpG ratio - Obs/Exp = (CpG count * window length) / (C count * G count), the standard formula - both clear their threshold. Every scanned window is independent ; consecutive or overlapping qualifying windows are then merged into a single island, whose own gcContent/observedToExpectedRatio are recomputed over its full merged span rather than inherited from whichever window first qualified, so they describe the island actually reported. Reuses SkewCalculator for the GC content half of the criteria rather than re-counting bases a second time.