NucleotideAmbiguityScoring.php
IUPAC-aware nucleotide substitution scoring Freely inspired by BioPHP's project biophp.org Created 9 October 2026 Last modified 9 October 2026
Table of Contents
Classes
- NucleotideAmbiguityScoring
- Scores two nucleotides by the bases each may stand for. Two definite bases are a match or a mismatch ; when one of them is an ambiguity code (R, Y, S, W, K, M, B, D, H, V, N, X), the pair is a mismatch only if the two sets of bases share nothing (R against Y : A/G against C/T), and otherwise scores the intermediate "ambiguous" value, 0 by default - a read that says N neither confirms nor refutes the base facing it, where SimpleMatchMismatchScoring gives N against N a full match and R against A a full mismatch. U is read as T, so DNA and RNA score alike. Case insensitive.