Alignment III PAM Matrices. PAM250 scoring matrix. 0. + 3. + ( -3 ). + 1. Scoring Matrices. S = [s ij ] gives score of aligning character i with character j for every pair i, j. S T P P C T C A. = 1. Scoring with a matrix.
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Two changesPAM matrices are based on a simple evolutionary model
Define a family of substitution matrices — PAM 1, PAM 2, etc. — where PAM n is used to compare sequences at distance n PAM.
PAM n = (PAM 1)n
Do not confuse with scoring matrices!
Scoring matrices are derived from PAM matrices to yield log-odds scores.
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