PHAT: a transmembrane-specific substitution matrix

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Predicting Functional Effect of Human Missense Mutations Using PolyPhen-2 (2013, methodology): “PolyPhen-2 7.20.28 Supplement 76 Current Protocols in Human Genetics PHAT score PHAT trans-membrane speciﬁc matrix (Ng et al., 2000) Measures effect of substitutions in trans-membrane regions; only used for positions annotated as trans-membrane.”
Domain enhanced lookup time accelerated BLAST (2012, background): “Sequence similarity searches generally perform better at detecting distantly related homologs when they use either matrices specialized for particular protein classes [3-11], or positionspecific score matrices (PSSMs) [12-23].”
Performance of mutation pathogenicity prediction methods on missense variants (2011, background): “…includes SWALL database [Johnson and Todd, 2000] annotations for sequence features, a transmembrane predictor TMHMM [Krogh et al., 2001] and PHAT [Ng et al., 2000] transmembrane-specific matrix score for substitutions at predicted transmembrane regions, the Coils2 program [Lupas et al., 1991]…”
SNAP: predict effect of non-synonymous polymorphisms on function (2007, background): “An additional sixth node was added to represent the difference between scores of wild-type and mutant residues in the PHAT matrix of transmembrane substitutions (50) if the residue was annotated to be part of the transmembrane region.”