Table 2.
In Silico Predictive Algorithms
| Missense prediction |
Name | Website | Basis |
|---|---|---|---|
| ConSurf | http://consurftest.tau.ac.il | Evolutionary conservation | |
| FATHMM | http://fathmm.biocompute.org.uk | Evolutionary conservation | |
| MutationAssessor | http://mutationassessor.org | Evolutionary conservation | |
| PANTHER | http://www.pantherdb.org/tools/csnpScoreForm.jsp | Evolutionary conservation | |
| PhD-SNP | http://snps.biofold.org/phd-snp/phd-snp.html | Evolutionary conservation | |
| SIFT | http://sift.jcvi.org | Evolutionary conservation | |
| SNPs&GO | http://snps-and-go.biocomp.unibo.it/snps-and-go | Protein structure/function | |
| Align GVGD | http://agvgd.iarc.fr/agvgd_input.php | Protein structure/function and evolutionary conservation |
|
| MAPP | http://mendel.stanford.edu/SidowLab/downloads/MAPP/index.html | Protein structure/function and evolutionary conservation |
|
| MutationTaster | http://www.mutationtaster.org | Protein structure/function and evolutionary conservation |
|
| MutPred | http://mutpred.mutdb.org | Protein structure/function and evolutionary conservation |
|
| PolyPhen-2 | http://genetics.bwh.harvard.edu/pph2 | Protein structure/function and evolutionary conservation |
|
| PROVEAN | http://provean.jcvi.org/index.php | Alignment and measurement of similarity between variant sequence and protein sequence homolog |
|
| nsSNPAnalyzer | http://snpanalyzer.uthsc.edu | Multiple sequence alignment and protein structure analysis |
|
| Condel | http://bg.upf.edu/condel/home | Combines SIFT, PolyPhen-2 and MutationAssessor |
|
| CADD | http://cadd.gs.washington.edu | Contrasts annotations of fixed/nearly fixed derived alleles in humans with simulated variants |
|
| Splice site prediction |
|||
| GeneSplicer | http://www.cbcb.umd.edu/software/GeneSplicer/gene_spl.shtml | Markov models | |
| Human Splicing Finder |
http://www.umd.be/HSF | Position-dependent logic | |
| MaxEntScan | http://genes.mit.edu/burgelab/maxent/Xmaxentscan_scoreseq.html | Maximum entropy principle | |
| NetGene2 | http://www.cbs.dtu.dk/services/NetGene2 | Neural networks | |
| NNSplice | http://www.fruitfly.org/seq_tools/splice.html | Neural networks | |
| FSPLICE | http://www.softberry.com/berry.phtml?topic=fsplice&group=programs&subgroup=gfind | ||
| Nucleotide conservation prediction |
|||
| GERP | http://mendel.stanford.edu/sidowlab/downloads/gerp/index.html | ||
| PhastCons | http://compgen.bscb.cornell.edu/phast/ | ||
| PhyloP | http://compgen.bscb.cornell.edu/phast/ |
In-silico tools/software prediction programs used for sequence variant interpretation