Table 1.
Summary of methods to predict the pathogenicity of mutations.
| Method | Main features | Further information |
|---|---|---|
| SIFT (Ng and Henikoff, 2001) | Threshold-based, conservation | http://sift.jcvi.org |
| PMUT (Ferrer-Costa et al., 2005) | Neural Network, sequence-, and structure-based features | http://mmb.pcb.ub.es/PMut |
| SNPs3D (Yue et al., 2006) | Support Vector Machine, structure-based features | http://www.snps3d.org |
| PANTHER (Thomas et al., 2003) | Threshold-based, conservation (PSEC) | http://www.pantherdb.org/tools/csnpScoreForm.jsp |
| Pfam LogRE (Clifford et al., 2004) | Threshold-based, probability of a PFAM domain to be pathogenic using a log-odds ratio | |
| LS-SNP (Karchin, 2009) | Support Vector Machine, sequence-, and structure-based features | http://ls-snp.icm.jhu.edu/ls-snp-pdb |
| CanPredict (Kaminker et al., 2007a) | Combines SIFT, Pfam LogRE, and Gene Ontology terms in a single prediction | http://research-public.gene.com/Research/genentech/canpredict |
| SNAP (Bromberg and Rost, 2007) | Neural Network, sequence-, and structure-based features | http://cubic.bioc.columbia.edu/services/snap |
| Torkamani (Torkamani and Schork, 2007) | Support Vector Machine, sequence-, and structure-based features, kinase-specific | |
| MutaGeneSys (Stoyanovich and Pe’er, 2008) | Whole-genome marker correlation dataset to identify association to causal SNPs in OMIM | http://www.cs.columbia.edu/~jds1/MutaGeneSys |
| stSNP (Uzun et al., 2007) | Integrates non-synonymous SNPs from dbSNP, structural models from Modeler and KEGG pathways. Comparative native/mutant analysis | http://ilyinlab.org/StSNP |
| F-SNP (Lee and Shatkay, 2008) | Metaserver, combines PolyPhen, SNPeffect2.0, SNPs3D, LS-SNP | http://compbio.cs.queensu.ca/F-SNP |
| SNP & GO (Calabrese et al., 2009) | Support Vector Machine, several sequence-derived features, and information from Gene Ontology terms | http://snps-and-go.biocomp.unibo.it/snps-and-go/ |
| PolyPhen-2 (Adzhubei et al., 2010) | Bayesian classifier, sequence-, and structure-based features | http://genetics.bwh.harvard.edu/pph2 |
| MuD (Wainreb et al., 2010) | Random forest, sequence-, and structure-based features | http://mud.tau.ac.il |
| CHASM (Wong et al., 2011) | Random forest, sequence-based features | http://wiki.chasmsoftware.org/index.php |
| Mutation Assessor (Reva et al., 2011) | Threshold-based, differential evolutionary conservation in subfamilies | http://mutationassessor.org |
| Condel (González-Pérez and López-Bigas, 2011) | Metaserver, combines the output of other predictors | http://bg.upf.edu/condel/ |
| wKinMut (Izarzugaza et al., 2012, submitted) | Framework for the analysis of kinase mutations. Integrates annotations, predictions, and information from the literature | http://wkinmut.bioinfo.cnio.es |