Amir

Variants Predictor Tools
With (Link to Web @ publication)
Tool and link summary publication
ActiveDriverDB
ActiveDriverDB: human disease mutations and
genome variation in post-translational modification
sites of proteins
10.1093/nar/gkx973
AGGRESCAN
AGGRESCAN: A server for the prediction and
evaluation of "hot spots" of aggregation in
polypeptides
10.1186/1471-2105-8-65
AGGRESCAN3D
AGGRESCAN3D (A3D): Server for prediction of
aggregation properties of protein structures
10.1093/nar/gkv359
Align-GVGD
Comprehensive statistical study of 452 BRCA1
missense substitutions with classification of eight
recurrent substitutions as neutral
10.1136/jmg.2005.033878
ALoFT
Using ALoFT to determine the impact of putative
loss-of-function variants in protein-coding genes
10.1038/s41467-017-00443-5
ANNOVAR
Genomic variant annotation and prioritization with
ANNOVAR and wANNOVAR
10.1038/nprot.2015.105
ASP/ASPex
The use of orthologous sequences to predict the
impact of amino acid substitutions on protein
function
10.1371/journal.pgen.1000968
ASSEDA
Automated splicing mutation analysis by information
theory
10.1002/humu.20151
AUTO-MUTE
AUTO-MUTE: Web-based tools for predicting stability
changes in proteins due to single amino acid
replacements
10.1093/protein/gzq042
AVIA
AVIA v2.0: Annotation, visualization and impact
analysis of genomic variants and genes
10.1093/bioinformatics/btv200
BeAtMuSiC
BeAtMuSiC: Prediction of changes in protein-protein
binding affinity on mutations.
10.1093/nar/gkt450
CADD
A general framework for estimating the relative
pathogenicity of human genetic variants
10.1038/ng.2892
CanDrA
CanDrA: Cancer-specific driver missense mutation
annotation with optimized features
10.1371/journal.pone.0077945
CanPredict
CanPredict: A computational tool for predicting
cancer-associated missense mutations
10.1093/nar/gkm405
CAROL
A combined functional annotation score for non-
synonymous variants
10.1159/000334984

CHASM
CHASM and SNVBox: Toolkit for detecting
biologically important single nucleotide mutations in
cancer
10.1093/bioinformatics/btr357
CHESS
A fully-automated event-
based variant prioritizing solution to
the CAGI5 intellectual disabilitygene panel challenge
10.1002/humu.23781
ChroMoS
ChroMoS: An integrated web tool for SNP
classification, prioritization and functional
interpretation
10.1093/bioinformatics/btt356
ClinPred
ClinPred: Prediction Tool to Identify Disease-
Relevant Nonsynonymous Single-Nucleotide
Variants
10.1016/j.ajhg.2018.08.005
ClinVar
ClinVar: Public archive of interpretations of clinically
relevant variants
10.1093/nar/gkv1222
CoDP
CoDP: Predicting the impact of unclassified genetic
variants in MSH6 by the combination of different
properties of the protein
10.1186/1423-0127-20-25
CoMEt
CoMEt: A statistical approach to identify
combinations of mutually exclusive alterations in
cancer
10.1186/s13059-015-0700-7
Condel
Improving the assessment of the outcome of
nonsynonymous SNVs with a consensus
deleteriousness score, Condel
10.1016/j.ajhg.2011.03.004
COSMIC
COSMIC: The Catalogue Of Somatic Mutations In
Cancer
10.1093/nar/gky1015
CoVEC
Predicting the functional consequences of non-
synonymous DNA sequence variants - evaluation of
bioinformatics tools and development of a
consensus strategy
10.1016/j.ygeno.2013.06.005
CUPSAT
Computational modeling of protein mutant stability:
Analysis and optimization of statistical potentials
and structural features reveal insights into prediction
model development
10.1186/1472-6807-7-54
DANN
DANN: A deep learning approach for annotating the
pathogenicity of genetic variants
10.1093/bioinformatics/btu703
DBD-Hunter
DBD-Hunter: A knowledge-based method for the
prediction of DNA-protein interactions
10.1093/nar/gkn332

dbNSFP
dbNSFP v3.0: A One-Stop Database of Functional
Predictions and Annotations for Human
Nonsynonymous and Splice-Site SNVs
10.1002/humu.22932
dbscSNV
In silico prediction of splice-altering single
nucleotide variants in the human genome
10.1093/nar/gku1206
dbSNP dbSNP: the NCBI database of genetic variation. 10.1093/nar/29.1.308
dbVar
dbVar and DGVa: Public archives for genomic
structural variation
10.1093/nar/gks1213
DDIG_in
Investigating DNA-, RNA-, and protein-based features
as a means to discriminate pathogenic synonymous
variants
10.1002/humu.23283
DeepSEA
Predicting effects of noncoding variants with deep
learning-based sequence model
10.1038/nmeth.3547
DFIRE/DDNA2
An all-atom knowledge-based energy function for
protein-DNA threading, docking decoy
discrimination, and prediction of transcription-factor
binding profiles
10.1002/prot.22384
Dmutant
Distance-scaled, finite ideal-gas reference state
improves structure-derived potentials of mean force
for structure selection and stability prediction
10.1110/ps.0217002
DUET
DUET: A server for predicting effects of mutations on
protein stability using an integrated computational
approach
10.1093/nar/gku411
EFIN
EFIN: Predicting the functional impact of
nonsynonymous single nucleotide polymorphisms in
human genome
10.1186/1471-2164-15-455
EGAD
Energy functions for protein design: Adjustment with
protein-protein complex affinities, models for the
unfolded state, and negative design of solubility and
specificity
10.1016/j.jmb.2004.12.019
EIGEN
A spectral approach integrating functional genomic
annotations for coding and noncoding variants
10.1038/ng.3477
Eris Eris: An automated estimator of protein stability [2] 10.1038/nmeth0607-466
EVmutation
Mutation effects predicted from sequence co-
variation
10.1038/nbt.3769

ExPecto
Deep learning sequence-based ab initio prediction of
variant effects on expression and disease risk.
10.1038/s41588-018-0160-6
Exome Variant
Server (EVS)
A map of human genome variation from population-
scale sequencing
10.1038/nature09534
Exomiser
Next-generation diagnostics and disease-gene
discovery with the Exomiser
10.1038/nprot.2015.124
FATHmm
Ranking non-synonymous single nucleotide
polymorphisms based on disease concepts
10.1186/1479-7364-8-11
fathmm-MKL
An integrative approach to predicting the functional
effects of non-coding and coding sequence variation
FIS
Predicting the functional impact of protein
mutations: Application to cancer genomics
10.1093/nar/gkr407
fitCons
A method for calculating probabilities of fitness
consequences for point mutations across the human
genome
10.1038/ng.3196
FOLD-RATE
FOLD-RATE: Prediction of protein folding rates from
amino acid sequence
10.1093/nar/gkl043
FoldAmyloid
FoldAmyloid: A method of prediction of
amyloidogenic regions from protein sequence
10.1093/bioinformatics/btp691
FOLDEF (core of
FOLDX)
The FoldX web server: an online force field 10.1093/nar/gki387
FunSAV
FunSAV: Predicting the functional effect of single
amino acid variants using a two-stage random forest
model
10.1371/journal.pone.0043847
GeneTests
GeneTests-GeneClinics: Genetic testing information
for a growing audience
10.1002/humu.10069
GenoCanyon
A statistical framework to predict functional non-
coding regions in the human genome through
integrated analysis of annotation data
10.1038/srep10576
GERP++
Identifying a high fraction of the human genome to be
under selective constraint using GERP++
10.1371/journal.pcbi.1001025
GWAVA
Functional annotation of noncoding sequence
variants
10.1038/nmeth.2832
HANSA
Hansa: An automated method for discriminating
disease and neutral human nsSNPs
10.1002/humu.21642

HGMD
The Human Gene Mutation Database: towards a
comprehensive repository of inherited mutation data
for medical research, genetic diagnosis and next-
generation sequencing studies
10.1007/s00439-017-1779-6
HMMvar
Predicting the combined effect of multiple genetic
variants
10.1186/s40246-015-0040-4
HOPE
HOPE: A homotopy optimization method for protein
structure prediction
10.1089/cmb.2005.12.1275
Human Splicing
Finder
Human Splicing Finder: An online bioinformatics tool
to predict splicing signals
10.1093/nar/gkp215
IMHOTEP
IMHOTEP-a composite score integrating popular
tools for predicting the functional consequences of
non-synonymous sequence variants
10.1093/nar/gkw886
INPS-3D
INPS-MD: A web server to predict stability of protein
variants from sequence and structure
10.1093/bioinformatics/btw192
INSIGHT
Application of a 5-tiered scheme for standardized
classification of 2,360 unique mismatch repair gene
variants in the InSiGHT locus-specific database
10.1038/ng.2854
is-rSNP
is-rSNP: A novel technique for in silico regulatory
SNP detection
10.1093/bioinformatics/btq378
K-FOLD
K-Fold: A tool for the prediction of the protein folding
kinetic order and rate
10.1093/bioinformatics/btl610
KD4i
A comprehensive study of small non-frameshift
insertions/deletions in proteins and prediction of
their phenotypic effects by a machine learning
method (KD4i)
10.1186/1471-2105-15-111
KGGSeq
Cepip: Context-dependent epigenomic weighting for
prioritization of regulatory variants and disease-
associated genes
10.1186/s13059-017-1177-3
KvSNP
Physicochemical constraint violation by missense
substitutions mediates impairment of protein
function and disease severity
10.1101/gr.3804205
LocTree LocTree3 prediction of localization 10.1093/nar/gku396
LOFTEE
Variation across 141,456 human exomes and
genomes reveals the spectrum of loss-of-function
intolerance across human protein-coding genes
10.1101/531210

LOVD/LSDB
LOVD v.2.0: The next generation in gene variant
databases
10.1002/humu.21438
LS-SNP/PDB
LS-SNP/PDB: Annotated non-synonymous SNPs
mapped to Protein Data Bank structures
MAESTRO
MAESTRO--multi agent stability prediction upon
point mutations
10.1186/s12859-015-0548-6
MAPP
Physicochemical constraint violation by missense
substitutions mediates impairment of protein
function and disease severity
10.1101/gr.3804205
MAPPIN
MAPPIN: A method for annotating, predicting
pathogenicity and mode of inheritance for
nonsynonymous variants
10.1093/nar/gkx730
MaxEnt
Maximum entropy modeling of short sequence motifs
with applications to RNA splicing signals
10.1089/1066527041410418
MetaLR
Comparison and integration of deleteriousness
prediction methods for nonsynonymous SNVs in
whole exome sequencing studies
10.1093/hmg/ddu733
MetaSVM
Comparison and integration of deleteriousness
prediction methods for nonsynonymous SNVs in
whole exome sequencing studies
10.1093/hmg/ddu733
MMSplice
MMSplice: modular modeling improves the
predictions of genetic variant effects on splicing
10.1186/s13059-019-1653-z
MultiMutate Four-body scoring function for mutagenesis 10.1093/bioinformatics/btm481
Mupro
Prediction of protein stability changes for single-site
mutations using support vector machines
10.1002/prot.20810
MuSiC
MuSiC: Identifying mutational significance in cancer
genomes
10.1101/gr.134635.111
MuStab
Sequence feature-based prediction of protein
stability changes upon amino acid substitutions
10.1186/1471-2164-11-s2-s5
MutationAssessor
Predicting the functional impact of protein
mutations: Application to cancer genomics
10.1093/nar/gkr407
MutationTaster
Mutationtaster2: Mutation prediction for the deep-
sequencing age
10.1038/nmeth.2890
MutPred Splice
MutPred Splice: Machine learning-based prediction
of exonic variants that disrupt splicing
10.1186/gb-2014-15-1-r19

MutPred-LOF
When loss-of-function is loss of function: Assessing
mutational signatures and impact of loss-of-function
genetic variants
10.1093/bioinformatics/btx272
MutPred2
Automated inference of molecular mechanisms of
disease from amino acid substitutions
MutPred2
MutPred2: inferring the molecular and phenotypic
impact of amino acid
10.1101/134981
MutSigCV
Mutational heterogeneity in cancer and the search for
new cancer-associated genes
10.1038/nature12213
MuX-48
Robust prediction of mutation-induced protein
stability change by property encoding of amino acids
10.1093/protein/gzn063
MuX-S
Robust prediction of mutation-induced protein
stability change by property encoding of amino acids
10.1093/protein/gzn063
NeEMO
NeEMO: A method using residue interaction
networks to improve prediction of protein stability
upon mutation
10.1186/1471-2164-15-s4-s7
NETdiseaseSNP
Prediction of Disease Causing Non-Synonymous
SNPs by the Artificial Neural Network Predictor
NetDiseaseSNP
10.1371/journal.pone.0068370
nsSNPAnalyzer
nsSNPAnalyzer: Identifying disease-associated
nonsynonymous single nucleotide polymorphisms
10.1093/nar/gki372
OMIM Online Mendelian Inheritance in Man (OMIM)
10.1002/(SICI)1098-
1004(200001)15
OncodriveCLUST
OncodriveCLUST: Exploiting the positional
clustering of somatic mutations to identify cancer
genes
PAGE
Prediction of aggregation rate and aggregation-prone
segments in polypeptide sequences
10.1110/ps.051471205
Panther
PANTHER version 11: Expanded annotation data
from Gene Ontology and Reactome pathways, and
data analysis tool enhancements
10.1093/nar/gkw1138
PantherPSEP
PANTHER-PSEP: Predicting disease-causing genetic
variants using position-specific evolutionary
preservation

Parepro
Predicting the phenotypic effects of non-
synonymous single nucleotide polymorphisms
based on support vector machines
10.1186/1471-2105-8-450
PASTA2
PASTA 2.0: An improved server for protein
aggregation prediction
10.1093/nar/gku399
PEPSI
Using secondary structure to predict the effects of
genetic variants on alternative splicing
10.1002/humu.23790
Personal Genome
Project
Privacy risks from genomic data-sharing beacons 10.1016/j.ajhg.2015.09.010
PharmGKB
PharmGKB: The pharmacogenomics knowledge
base
10.1007/978-1-62703-435-7_20
phastCons
Evolutionarily conserved elements in vertebrate,
insect, worm, and yeast genomes
10.1101/gr.3715005
PhD-SNP
Predicting the insurgence of human genetic diseases
associated to single point protein mutations with
support vector machines and evolutionary
information
10.1093/bioinformatics/btl423
Phen-Gen
Phen-gen: Combining phenotype and genotype to
analyze rare disorders
10.1038/nmeth.3046
phyloP
Detection of nonneutral substitution rates on
mammalian phylogenies
10.1101/gr.097857.109
PMUT
PMut: A web-based tool for the annotation of
pathological variants on proteins, 2017 update
10.1093/nar/gkx313
PolyPhen
A method and server for predicting damaging
missense mutations
10.1038/nmeth0410-248
PON_Diso
Performance of Protein Disorder Prediction
Programs on Amino Acid Substitutions
10.1002/humu.22564
PON_mt_tRNA
PON-mt-tRNA: A multifactorial probability-based
method for classification of mitochondrial tRNA
variations
10.1093/nar/gkw046
PON-P2
PON-P2: Prediction method for fast and reliable
identification of harmful variants
10.1371/journal.pone.0117380
PopMuSic
PoPMuSiC 2.1: A web server for the estimation of
protein stability changes upon mutation and
sequence optimality
10.1186/1471-2105-12-151

PPT-DB
PPT-DB: The protein property prediction and testing
database
10.1093/nar/gkm800
PredictSNP2
PredictSNP2: A Unified Platform for Accurately
Evaluating SNP Effects by Exploiting the Different
Characteristics of Variants in Distinct Genomic
Regions.
10.1371/journal.pcbi.1004962
ProA
Identification of properties important to protein
aggregation using feature selection
10.1186/1471-2105-14-314
PROFcon PROFcon: Novel prediction of long-range contacts 10.1093/bioinformatics/bti454
PROVEAN
PROVEAN web server: A tool to predict the functional
effect of amino acid substitutions and indels
QueryOR
QueryOR: A comprehensive web platform for genetic
variant analysis and prioritization
10.1186/s12859-017-1654-4
REMM
A Whole-Genome Analysis Framework for Effective
Identification of Pathogenic Regulatory Variants in
Mendelian Disease
10.1016/j.ajhg.2016.07.005
REVEL
REVEL: An Ensemble Method for Predicting the
Pathogenicity of Rare Missense Variants
10.1016/j.ajhg.2016.08.016
SAAPdap/SAAPred
The SAAPdb web resource: A large-scale structural
analysis of mutant proteins
10.1002/humu.20898
SAPred
Finding new structural and sequence attributes to
predict possible disease association of single amino
acid polymorphism (SAP)
10.1093/bioinformatics/btm119
Scide
SCide: Identification of stabilization centers in
proteins
10.1093/bioinformatics/btg110
Scpred
SCPRED: Accurate prediction of protein structural
class for sequences of twilight-zone similarity with
predicting sequences
10.1186/1471-2105-9-226
SDM
SDM: A server for predicting effects of mutations on
protein stability
10.1093/nar/gkx439
SDS
SDS, a structural disruption score for assessment of
missense variant deleteriousness
10.3389/fgene.2014.00082
SeqVItA
SeqVItA: Sequence Variant Identification and
Annotation Platform for Next Generation Sequencing
Data
10.3389/fgene.2018.00537

SIFT
SIFT web server: Predicting effects of amino acid
substitutions on proteins
10.1093/nar/gks539
SIFT-indel
SIFT Indel: Predictions for the Functional Effects of
Amino Acid Insertions/Deletions in Proteins
10.1371/journal.pone.0077940
SignalP
SignalP 4.0: Discriminating signal peptides from
transmembrane regions
10.1038/nmeth.1701
SilVA
Identification of deleterious synonymous variants in
human genomes
SInBaD
Exploring functional variant discovery in non-coding
regions with SInBaD
10.1093/nar/gks800
SiPhy
Identifying novel constrained elements by exploiting
biased substitution patterns
Skippy
Genomic features defining exonic variants that
modulate splicing
10.1186/gb-2010-11-2-r20
SNAP2
Better prediction of functional effects for sequence
variants
10.1186/1471-2164-16-s8-s1
SNPedia
SNPedia: A wiki supporting personal genome
annotation, interpretationand analysis
10.1093/nar/gkr798
SNPdbe
Snpdbe: Constructing an nsSnp functional impacts
database
10.1093/bioinformatics/btr705
SnpEff
A program for annotating and predicting the effects
of single nucleotide polymorphisms, SnpEff: SNPs in
the genome of Drosophila melanogaster strain
w1118; iso-2; iso-3
10.4161/fly.19695
SNPeffect
SNPeffect 4.0: On-line prediction of molecular and
structural effects of protein-coding variants
10.1093/nar/gkr996
SNPinfo/FuncPred
SNPinfo: Integrating GWAS and candidate gene
information into functional SNP selection for genetic
association studies
10.1093/nar/gkp290
SNPnexus?
SNPnexus: Assessing the functional relevance of
genetic variation to facilitate the promise of precision
medicine
10.1093/nar/gky399
SNPs3D
Predicting the phenotypic effects of non-
synonymous single nucleotide polymorphisms
based on support vector machines
10.1186/1471-2105-8-450

SPANR/SPIDEX
The human splicing code reveals new insights into
the genetic determinants of disease.
10.1126/science.1254806
SPF_Cancer
A new disease-specific machine learning approach
for the prediction of cancer-causing missense
variants
10.1016/j.ygeno.2011.06.010
SuRFR
SuRFing the genomics wave: An R package for
prioritising SNPs by functionality
10.1186/s13073-014-0079-1
SVScore
SVScore: an impact prediction tool for structural
variation
Syntool
Syntool: A novel region-based intolerance score to
single nucleotide substitution for synonymous
mutations predictions based on 123,136 individuals
10.1155/2017/5096208
TANGO
Protein aggregation and amyloidosis: Confusion of
the kinds?
10.1016/j.sbi.2006.01.011
TransComp
Automated prediction of protein association rate
constants
10.1016/j.str.2011.10.015
transFIC
Improving the prediction of the functional impact of
cancer mutations by baseline tolerance
transformation
10.1186/gm390
UMD-predictor
UMD-predictor, a new prediction tool for nucleotide
substitution pathogenicity - Application to four
genes: FBN1, FBN2, TGFBR1, and TGFBR2
10.1002/humu.20970
VAAST
VAAST 2.0: Improved variant classification and
disease-gene identification using a conservation-
controlled amino acid substitution matrix
10.1002/gepi.21743
Variant Tools
Reproducible simulations of realistic samples for
next-generation sequencing studies using variant
simulation tools
10.1002/gepi.21867
VariBench VariBench: A Benchmark Database for Variations 10.1002/humu.22204
VariSNP
VariSNP, A benchmark database for variations from
dbSNP
10.1002/humu.22727
VarMod
VarMod: Modelling the functional effects of non-
synonymous variants
10.1093/nar/gku483
VarWalker
VarWalker: Personalized Mutation Network Analysis
of Putative Cancer Genes from Next-Generation
Sequencing Data
10.1371/journal.pcbi.1003460

VEP The Ensembl Variant Effect Predictor 10.1186/s13059-016-0974-4
VEST
Identifying Mendelian disease genes with the Variant
Effect Scoring Tool
10.1186/1471-2164-14-s3-s3
VEST-indel
Assessing the Pathogenicity of Insertion and
Deletion Variants with the Variant Effect Scoring Tool
(VEST-Indel)
10.1002/humu.22911
Waltz
Exploring the sequence determinants of amyloid
structure using position-specific scoring matrices
10.1038/nmeth.1432
WGSA
WGSA: An annotation pipeline for human genome
sequencing studies
10.1136/jmedgenet-2015-
103423
wInterVar
InterVar: Clinical Interpretation of Genetic Variants
by the 2015 ACMG-AMP Guidelines
10.1016/j.ajhg.2017.01.004
WoLF-PSORT WoLF PSORT: Protein localization predictor 10.1093/nar/gkm259
WS-SNPs&GO
WS-SNPs&GO: a web server for predicting the
deleterious effect of human protein variants using
functional annotation
10.1186/1471-2164-14-s3-s6
Zyggregator
The Zyggregator method for predicting protein
aggregation propensities
10.1039/b706784b
https://ampliseq.com/search.action
link to search Ion AmpliSeq Designer

Amir

Recommended

Recommended

More Related Content

What's hot

What's hot (6)

Similar to Amir

Similar to Amir (20)

Recently uploaded

Recently uploaded (20)

Amir