Pam250Scoring.php
PAM250 substitution matrix scoring Freely inspired by BioPHP's project biophp.org Created 30 September 2026 Last modified 9 October 2026
Table of Contents
Classes
- Pam250Scoring
- Scores a pair of amino acid symbols using the PAM250 substitution matrix already exposed by bioapi for other parts of this library (see Api\Pam250MatrixDigitApi), rather than a flat match/mismatch rule. The matrix is fetched and flattened once, in the constructor, and is exhaustive for every ordered pair of the twenty standard amino acids ; it has no entry for any other symbol AminoAcidSequence tolerates - the ambiguous B, Z, J and X, selenocysteine U, pyrrolysine O and the stop "*" - which score() reports as an error rather than guessing a value.