Prediction of Deleterious Nonsynonymous Single-Nucleotide Polymorphism for Human Diseases

Table 2

Tools for deleterious variant detection.

Method	Website	Features	Method description	Reference ID
SIFT	http://sift.bii.a-star.edu.sg/	Sequence based	Statistical method using PSSM with Dirichlet priors	[17]
PolyPhen	http://genetics.bwh.harvard.edu/pph/index.html	Sequence based, structure based, annotation	Rule-based model	[2]
SNAP	http://www.rostlab.org/services/SNAP/	Sequence based, annotation	Standard feed-forward neural networks with momentum term	[1]
MSRV	http://bioinfo.au.tsinghua.edu.cn/member/ruijiang/english/software.html	Sequence based	Multiple selection rule voting strategy using random forest	[11]
LRT	http://www.genetics.wustl.edu/jflab/lrt_query.html	Sequence based	Log ratio test	[19]
PolyPhen-2	http://genetics.bwh.harvard.edu/pph2/index.shtml	Sequence based, structure based	Naïve Bayes approach coupled with entropy-based discretization	[18]
MutationTaster	http://www.mutationtaster.org/	Sequence based, annotation	Naïve bayes model based on integrated data source	[5]
KGGSeq	http://statgenpro.psychiatry.hku.hk/limx/kggseq/	Sequence based, annotation	A three-level framework to combine a number of filtration and prioritization functions	[23]
SInBaD	http://tingchenlab.cmb.usc.edu/sinbad/	Sequence based	Separate mathematical models for promoters, exons, and introns, using logistic regression algorithm	[21]
GERP (score)	http://mendel.stanford.edu/sidowlab/downloads/gerp/index.html	Sequence based	A “Rejected Substitutions” score computation to infer the constrained region	[24]
PhyloP (score)	http://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way	Sequence based	An exact 𝑃 value computation under a continuous Markov substitution model	[10]