Skip to main content
. Author manuscript; available in PMC: 2014 Jul 24.
Published in final edited form as: Hum Mutat. 2013 Jul 10;34(9):E2393–E2402. doi: 10.1002/humu.22376

Table 2.

A summary of functional prediction scores and conservation scores.

Score Training data Information used Prediction model
PolyPhen-2 UniProtKB/UniRef100; PDB/DSSP; UCSC alignments of 45 vertebrate genomes eight sequence-based and three structure-based predictive features naive Bayes classifier
SIFT SWISS-PROT/TrEMBL sequence homology based on PSI-BLAST position specific scoring matrix
Mutation Taster UniProt; homologous genes in humans and 10 other species; dbSNP; HapMap conservation, splice site, mRNA features, protein features; naive Bayes classifier
LRT coding sequences of 32 vertebrate species sequence homology likelihood ratio test of codon neutrality
Mutation Assessor homologous sequences from Uniprot identified by BLAST sequence homology of protein families and sub-families within and between species combinatorial entropy formalism
FATHMM homologous sequences from UniRef90, SUPERFAMILY and Pfam sequence homology hidden Markov models
SiPhy genomes of 29 mammals multiple alignments inferring nucleotide substitution pattern per site
GERP++ genomes of 34 mammals multiple alignments and phylogenetic tree maximum likelihood evolutionary rate estimation
PhyloP genomes of 33 placental mammals multiple alignments and phylogenetic tree distributions of the number of substitutions based on phylogenetic hidden Markov model
HHS Vulnerability Disclosure