Chunk #13 — Materials and Methods — Incorporating Species-Specific Pathogenicity Weights

Source

Predicting the functional, molecular, and phenotypic consequences of amino acid substitutions using hidden Markov models.

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where Pw and Pm represent the underlying probabilities for the wild-type and mutant amino acid residues, respectively, and the pathogenicity weights, Wd and Wn, represent the relative frequencies of disease-associated and functionally neutral AASs mapping onto the relevant HMM, respectively. The pathogenicity weights also include a pseudo-count of 1.0 to avoid a zero divisible term.