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Variant functional prediction software tools | Whole-genome sequencing data analysis

Modern sequencing technologies produce increasingly detailed data on genomic variation. However, conventional methods for relating either individual variants or mutated genes to phenotypes present known limitations given the complex, multigenic…
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MutationTaster
Web

MutationTaster

A free, web-based application for rapid evaluation of the disease-causing…

A free, web-based application for rapid evaluation of the disease-causing potential of DNA sequence alterations. MutationTaster integrates information from different biomedical databases and uses…

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SNPdryad
Web

SNPdryad

Predicts deleterious effect of amino acid substitutions occurred in human…

Predicts deleterious effect of amino acid substitutions occurred in human proteins. SNPdryad is a computational method that collects the orthologous protein sequences from other mammals and performs…

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GeneTalk
Web

GeneTalk

A web-based tool, knowledgebase and community for analysis and interpretation…

A web-based tool, knowledgebase and community for analysis and interpretation of human variant files. GeneTalk provides an intuitive web-based interface for geneticists that analyze human sequence…

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EVmutation
Desktop

EVmutation

Predicts the effects of mutations while taking into account the interactions…

Predicts the effects of mutations while taking into account the interactions that occur between amino acids in proteins or bases in RNA. EVmutation predicts the relative favourability of unseen…

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PolyPhen-2
Web
Desktop

PolyPhen-2 Polymorphism Phenotyping

Predicts possible impact of an amino acid substitution on the structure and…

Predicts possible impact of an amino acid substitution on the structure and function of a human protein using straightforward physical and comparative considerations. For a mutation, PolyPhen…

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SIFT
Web

SIFT Sorting Tolerant From Intolerant

Predicts whether an amino acid substitution affects protein function. SIFT…

Predicts whether an amino acid substitution affects protein function. SIFT prediction is based on the degree of conservation of amino acid residues in sequence alignments derived from closely related…

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PANTHER
Web

PANTHER Protein ANalysis THrough Evolutionary Relationships

A widely used online resource for comprehensive protein evolutionary and…

A widely used online resource for comprehensive protein evolutionary and functional classification, and includes tools for large-scale biological data analysis. The latest version of PANTHER, 10.0,…

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M-CAP
Web
Desktop

M-CAP Mendelian Clinically Applicable Pathogenicity

Represents a clinical pathogenicity classifier. M-CAP aims to misclassify no…

Represents a clinical pathogenicity classifier. M-CAP aims to misclassify no more than 5% of pathogenic variants while aggressively reducing the list of variants of uncertain significance. This tool…

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VEP
Web
Desktop

VEP Variant Effect Predictor

Determines the effect of your variants (SNPs, insertions, deletions, CNVs or…

Determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Simply input the…

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Hotspot3D
Desktop

Hotspot3D

Identifies such spatial hotspots (clusters) and interprets the potential…

Identifies such spatial hotspots (clusters) and interprets the potential function of variants within them. HotSpot3D is a computational tool which identifies mutation–mutation and mutation–drug…

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Eigen
Desktop

Eigen

An unsupervised spectral approach for scoring variants which does not make use…

An unsupervised spectral approach for scoring variants which does not make use of labeled training data. Eigen produces estimates of predictive accuracy for each functional annotation score, and…

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VEST
Desktop

VEST Variant Effect Scoring Tool

Allows to estimate a gene’s importance in human disease. The VEST method for…

Allows to estimate a gene’s importance in human disease. The VEST method for estimate gene importance can be applicable to missense and other bioinformatics pathogenicity predictors. It assess the…

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PROVEAN
Desktop
Web

PROVEAN Protein Variation Effect Analyzer

A software tool which predicts whether an amino acid substitution or indel has…

A software tool which predicts whether an amino acid substitution or indel has an impact on the biological function of a protein. PROVEAN is useful for filtering sequence variants to identify…

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Mutationassesso…
Web

Mutationassessor

Predicts the functional impact of amino-acid substitutions in proteins, such as…

Predicts the functional impact of amino-acid substitutions in proteins, such as mutations discovered in cancer or missense polymorphisms. The functional impact is assessed based on evolutionary…

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PredictSNP
Web

PredictSNP

Consensus classifiers for prediction of disease-related mutations. PredictSNP1…

Consensus classifiers for prediction of disease-related mutations. PredictSNP1 offers its users a consensus score based on the output of six different amino acid-based predictors. Because of the…

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dSysMap
Web

dSysMap

Displays Human disease-related mutations on the structural interactome. Mapping…

Displays Human disease-related mutations on the structural interactome. Mapping of mutations on protein structures and on interaction interfaces allows you to visualize the region of the interactome…

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SNAP
Web

SNAP Screening for Non-Acceptable Polymorphisms

A neural-network based tool to be used for the evaluation of functional effects…

A neural-network based tool to be used for the evaluation of functional effects single amino acid substitutions in proteins. SNAP utilizes various biophysical characteristics of the substitution, as…

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DDIG-Indel
Web

DDIG-Indel Detecting disease-causing genetic variations due to indels

A support vector machine-based method to prioritize non-frameshifting indels by…

A support vector machine-based method to prioritize non-frameshifting indels by comparing disease-associated mutations with putatively neutral mutations from the 1,000 Genomes Project. The final…

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FATHMM-XF
Web
Desktop

FATHMM-XF

Allows prediction of the functional consequences of non-coding and coding…

Allows prediction of the functional consequences of non-coding and coding single nucleotide variants (SNVs). FATHMM-XF is a method consisting in an improvement over the predictor FATHMM-MKL. The…

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GERP
Desktop

GERP Genomic Evolutionary Rate Profiling

Identifies constrained elements in multiple alignments by quantifying…

Identifies constrained elements in multiple alignments by quantifying substitution deficits.

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CHASM/SNV-Box
Desktop

CHASM/SNV-Box Cancer-specific High-throughput Annotation of Somatic Mutations

A software toolkit to prioritize SNVs based on their predicted contribution to…

A software toolkit to prioritize SNVs based on their predicted contribution to tumorigenesis. CHASM includes a database of pre-computed predictive features called SNVBox that facilitates rapid…

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Condel
Web

Condel CONsensus DELeteriousness score of missense SNVs

A method to assess the outcome of non-synonymous SNVs using a consensus…

A method to assess the outcome of non-synonymous SNVs using a consensus deleteriousness score that combines various tools (MutationAssessor, FATHMM). The simplicity of Condel allows it to be easily…

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SnpEff
Desktop
Web

SnpEff

Annotates and predicts the effects of single nucleotide polymorphisms (SNPs).…

Annotates and predicts the effects of single nucleotide polymorphisms (SNPs). SnpEff features include: (1) the ability to make thousands of predictions per second; (2) the ability to add custom…

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SNPs&GO
Web

SNPs&GO

Serves to the prediction of deleterious single amino acid polymorphisms (SAPs)…

Serves to the prediction of deleterious single amino acid polymorphisms (SAPs) using protein functional annotation. The WS-SNPs&GO web server is based on support vector machines (SVM) and for a…

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MAPP
Desktop

MAPP Multivariate Analysis of Protein Polymorphism

Quantifies the physicochemical variation in each column of a multiple sequence…

Quantifies the physicochemical variation in each column of a multiple sequence alignment and calculates the deviation of candidate amino acid replacements from this variation. The greater the…

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CRAVAT
Web

CRAVAT Cancer-Related Analysis of Variants Toolkit

Performs cancer-related analysis of variants. CRAVAT returns mutation…

Performs cancer-related analysis of variants. CRAVAT returns mutation interpretations in a dynamic interactive web environment for sorting, visualizing and inferring mechanism. The software (i)…

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proBAMr
Desktop

proBAMr

Maps peptide spectrum matches (PSMs) back to genome. proBAMr consists of three…

Maps peptide spectrum matches (PSMs) back to genome. proBAMr consists of three steps. First the peptide from a PSM is mapped to corresponding protein sequence, and its starting and ending positions…

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CAPE
Web
Desktop

CAPE CellulAr dePendent dEactivating mutations predictor

Provides a scoring scheme capable of accurately recognizing deleterious…

Provides a scoring scheme capable of accurately recognizing deleterious regulatory variants on a genome-wide scale. CAPE detects cellular dependent deactivating mutations and can prioritize…

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IMHOTEP
Web

IMHOTEP Integrating Molecular Heuristics and Other Tools for Effect Prediction

Predicts the functional consequences of mutations of human pathogenetics.…

Predicts the functional consequences of mutations of human pathogenetics. IMHOTEP integrates nine popular prediction tools (PolyPhen-2, SNPs&GO, MutPred, SIFT, MutationTaster2, Mutation Assessor…

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StructMAn
Web

StructMAn Structural Mutation Annotation

A web-based tool for annotation of human and non-human (non-synonymous) single…

A web-based tool for annotation of human and non-human (non-synonymous) single nucleotide variant (nsSNVs) in the structural context. StructMAn analyzes the spatial location of the amino acid residue…

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Align-GVGD
Web

Align-GVGD

A method that combines Grantham Variation (GV) and Grantham Deviation (GD)…

A method that combines Grantham Variation (GV) and Grantham Deviation (GD) scores to predict the transactivation activity of each missense substitution. We compared our predictions against…

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GAVIN
Web

GAVIN Gene-Aware Variant INterpretation

Delivers accurate and reliable automated classification of variants for…

Delivers accurate and reliable automated classification of variants for clinical application. GAVIN classifies variants as benign, pathogenic, or a variant of uncertain significance (VUS). It is able…

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DOMINO
Web

DOMINO

Allows detection of genes associated with dominant disorders. DOMINO is based…

Allows detection of genes associated with dominant disorders. DOMINO is based on linear discriminant analysis (LDA). It can efficiently prioritize candidate genes associated with autosomal dominant…

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MutPred
Web

MutPred

A web application tool developed to classify an amino acid substitution as…

A web application tool developed to classify an amino acid substitution as disease-associated or neutral in human. In addition, MutPred predicts molecular cause of disease. The tool requires a…

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PhD-SNP
Desktop
Web

PhD-SNP Predictor of human Deleterious Single Nucleotide Polymorphisms

A method based on support vector machines (SVMs) that starting from the protein…

A method based on support vector machines (SVMs) that starting from the protein sequence information can predict whether a new phenotype derived from a nsSNP can be related to a genetic disease in…

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PinSnps
Web

PinSnps

A practical computational pipeline to readily perform data analyses of…

A practical computational pipeline to readily perform data analyses of protein-protein interaction networks (PPINs) by using genetic and functional information mapped onto protein structures. We…

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deltaBS
Desktop

deltaBS

A sequence analysis method for predicting whether genome variation is likely to…

A sequence analysis method for predicting whether genome variation is likely to result in phenotypic differences, and an application of the method across a variety of analysis scales. Unlike…

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StSNP
Web

StSNP Structure SNP

Provides practical, user friendly access to the wealth of information related…

Provides practical, user friendly access to the wealth of information related to nsSNPs by seamlessly connecting various databases into one pipeline. Key functional and structural information along…

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SiPhy
Desktop

SiPhy

Implements rigorous statistical tests to detect bases under selection from a…

Implements rigorous statistical tests to detect bases under selection from a multiple alignment data.

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REVEL
Desktop

REVEL Rare Exome Variant Ensemble Learner

Predicts the pathogenicity of missense variants on the basis of individual…

Predicts the pathogenicity of missense variants on the basis of individual tools: MutPred, FATHMM, VEST, PolyPhen, SIFT, PROVEAN, MutationAssessor, MutationTaster, LRT, GERP, SiPhy, phyloP, and…

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KinMutRF
Desktop

KinMutRF

Identifies automatically pathogenic variants in human kinases. KinMutRF…

Identifies automatically pathogenic variants in human kinases. KinMutRF identifies disease-associated variants satisfactorily when trained and cross-validated with the 3689 human kinase variants from…

HyB_BR
Desktop

HyB_BR Hybrid BayesR

Allows users to perform simultaneous genomic prediction and quantitative trait…

Allows users to perform simultaneous genomic prediction and quantitative trait loci (QTL) mapping. Hyb_BR is developed as a hybrid algorithm which combine an Expectation-Maximisation (EM) module and…

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Frustration
Desktop

Frustration

A framework in which index frustration, quantifying unfavorable local…

A framework in which index frustration, quantifying unfavorable local interactions, is employed as a metric to investigate the effects of single-nucleotide variants. The frustration index quantifies…

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PVP
Desktop

PVP PhenomeNET Variant Predictor

Allows highly accurate genome-scale identification of causative variants…

Allows highly accurate genome-scale identification of causative variants involved in human disease. PVP is a system which annotates and prioritizes disease variants in whole exome sequencing (WES)…

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COCOS
Desktop

COCOS COdon COnsequence Scanner

Allows annotation of reading frame changes induced by stop-lost and frame-shift…

Allows annotation of reading frame changes induced by stop-lost and frame-shift variants. COCOS is a Variant Effect Predictor (VEP) plugin that captures variant induced codon alterations and presents…

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DEOGEN
Desktop

DEOGEN

Represents a novel method for variant-effect prediction that integrates…

Represents a novel method for variant-effect prediction that integrates heterogeneous sources of biological information. DEOGEN analyzes protein and variant pair by combining different levels of…

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LS-SNP/PDB
Web

LS-SNP/PDB

A web tool for genome-wide annotation of human SNPs. LS-SNP/PDB provides…

A web tool for genome-wide annotation of human SNPs. LS-SNP/PDB provides information useful for identifying amino-acid changing SNPs (nsSNPs) that are most likely to have an impact on biological…

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phyloP
Desktop

phyloP phylogenetic P-values

Computes conservation or acceleration p-values, either lineage-specific or…

Computes conservation or acceleration p-values, either lineage-specific or across all branches. phyloP was applied to multiple alignments of 36 species in the ENCODE regions and analyze patterns of…

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HOPE
Web

HOPE Have yOur Protein Explained

An easy-to-use web service that analyses the structural effects of a point…

An easy-to-use web service that analyses the structural effects of a point mutation in a protein sequence. Input your protein sequence and the mutation and HOPE will collect and combine available…

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wKinMut
Web

wKinMut

An integrated framework for the analysis and interpretation of the consequences…

An integrated framework for the analysis and interpretation of the consequences of variants in the human kinome. wKinMut web-server offers direct prediction of the potential pathogenicity of the…

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