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Regulatory variant detection software tools | Genome variation analysis

Genome-wide association studies revealed that most disease-associated single nucleotide polymorphisms (SNPs) are located in regulatory regions within introns or in regions between genes. Regulatory SNPs (rSNPs) are such SNPs that affect gene…
deltaSVM
Desktop

deltaSVM

A sequence-based computational method to predict the effect of regulatory…

A sequence-based computational method to predict the effect of regulatory variation, using a classifier (gkm-SVM) that encodes cell type-specific regulatory sequence vocabularies. The induced change…

MPRAnator
Desktop

MPRAnator Massively Parallel Reporter Assays

Facilitates rapid design of massively parallel reporter assays (MPRA)…

Facilitates rapid design of massively parallel reporter assays (MPRA) experiments. MPRAnator allows systematic design of MPRA experiments for the investigation of the effects of single nucleotide…

Sasquatch
Web
Desktop

Sasquatch

Identifies and quantifies footprints of the effects of noncoding variants on…

Identifies and quantifies footprints of the effects of noncoding variants on transcription factor (TF) binding. Sasquatch provides a relatively simple and yet informative approach, requiring only a…

HaploReg
Web

HaploReg

A tool for exploring annotations of the noncoding genome at variants on…

A tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes…

G T A T C G C T A
SNPhood
Desktop

SNPhood

A user-friendly Bioconductor R package to investigate, quantify and visualise…

A user-friendly Bioconductor R package to investigate, quantify and visualise the local epigenetic neighbourhood of a set of SNPs in terms of chromatin marks or transcription factor binding sites…

OncoCis
Web

OncoCis

A user friendly tool for annotating cancer mutations in cis-regulatory regions…

A user friendly tool for annotating cancer mutations in cis-regulatory regions of DNA. OncoCis integrates publicly available datasets representing a wide range of cancer types from genome-wide…

is-rSNP
Web

is-rSNP In silico regulatory SNP detection

Predicts whether a SNP is an rSNP. For a given SNP, and using a statistical…

Predicts whether a SNP is an rSNP. For a given SNP, and using a statistical framework, is-rSNP can successfully predict the set of TFs for which binding is affected. It provides the statistical power…

ePOSSUM
Web

ePOSSUM

Uses a Bayes classifier to assess the impact of genetic alterations on…

Uses a Bayes classifier to assess the impact of genetic alterations on transcription factor binding in user-defined sequences. ePOSSUM includes a measure of significance of the assessments to…

GenomeRunner
Web

GenomeRunner

An automated framework for the statistical analysis and interpretation of the…

An automated framework for the statistical analysis and interpretation of the functional impact of SNP sets using regulatory datasets from the ENCODE, Roadmap Epigenomics and other projects.…

RAVEN
Web

RAVEN Regulatory analysis of Variation in ENhancers

Searchs putative regulatory genetic variation in favorite gene. SNPs (from…

Searchs putative regulatory genetic variation in favorite gene. SNPs (from dbSNP and user defined) are analyzed for overlap with potential transcription factor binding sites (TFBS) and phylogenetic…

BayesPI-BAR
Desktop
GERV
Desktop

GERV Generative Evaluation of Regulatory Variants

A computational method for predicting regulatory variants that affect…

A computational method for predicting regulatory variants that affect transcription factor binding. GERV learns a k-mer-based generative model of transcription factor binding from ChIP-seq and…

rSNPs MAPPER
Web

rSNPs MAPPER

A powerful tool for the large-scale analysis of regulatory SNPs. Its main…

A powerful tool for the large-scale analysis of regulatory SNPs. Its main purpose is to evaluate the potential effect of a SNP on predicted transcription factor binding sites, by measuring the change…

RegulatorDB
Web

RegulatorDB

Permits users to analyze the mutant expression profiles and DNA-binding targets…

Permits users to analyze the mutant expression profiles and DNA-binding targets for nearly all regulators in Saccharomyces cerevisiae. By integrating DNA binding data and mutant expression profiles…

HPRS pipeline
Desktop

HPRS pipeline Human Projection of Regulatory Sequences pipeline

Predicts equivalent information in other mammalian species. HPRS pipeline…

Predicts equivalent information in other mammalian species. HPRS pipeline utilizes genomic and epigenomic data for human genome to realize these predictions. This tool can be used in the case of…

μ-cisTarget
Web

μ-cisTarget

Identifies cis-regulatory mutations in a cancer sample, but it can also to…

Identifies cis-regulatory mutations in a cancer sample, but it can also to filter, annotate and prioritize non coding-variants based on their putative effect on the underlying 'personal'…

PERFECTOS-APE
Desktop
Web
motifbreakR
Desktop

motifbreakR

An R package for predicting the disruptiveness of single nucleotide…

An R package for predicting the disruptiveness of single nucleotide polymorphisms on transcription factor binding sites. motifbreakR allows the biologist to judge whether the sequence surrounding a…

atSNP
Desktop

atSNP affinity testing for regulatory SNPs

A computationally efficient R package for identifying rSNPs in silico. atSNP…

A computationally efficient R package for identifying rSNPs in silico. atSNP implements an importance sampling algorithm coupled with a first-order Markov model for the background nucleotide…

TRAP
Desktop
Web

TRAP Transcription factor Affinity Prediction

Calculates the affinity of transcription factors for DNA sequences on the basis…

Calculates the affinity of transcription factors for DNA sequences on the basis of a biophysical model. This method has proven to be useful for several applications, including for determining the…

rSNPdect
Desktop

rSNPdect

Provides a method to distinguish Regulatory single nucleotide polymorphisms…

Provides a method to distinguish Regulatory single nucleotide polymorphisms (rSNPs) in human genome from massive background SNPs. rSNPdect is a Matlab package and a computational method for rSNP…

regSNPs
Desktop

regSNPs

An informatics strategy that integrates several established bioinformatics…

An informatics strategy that integrates several established bioinformatics tools, for prioritizing regulatory SNPs, i.e. the SNPs in the promoter regions that potentially affect phenotype through…

FIMO
Desktop
Web

FIMO Find Individual Motif Occurrences

A software tool for scanning DNA or protein sequences with motifs described as…

A software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices. The FIMO algorithm identifies all individual motif occurrences and is the method of…

SNPLogic
Web

SNPLogic

Brings together single nucleotide polymorphism (SNP) information from numerous…

Brings together single nucleotide polymorphism (SNP) information from numerous sources to provide a comprehensive SNP selection, annotation and prioritization system for design and analysis of…

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