Hello,
I have the SNPs ID list from the VEP Ensembl database based on the whole exome sequencing data I got in the literature. I want to know if there are any web-based tools that can analyze the SNPs SNPs' interaction using their rs ID?
Thank you
Asif Bilal
3DSNP Description : A database linking noncoding SNPs to 3D interacting genes. 4P Description : Computes population genetics statistics from large single nucleotide polymorphism (SNP) datasets. It also includes computation of the joint frequency spectrum. 4Pipe4 Description : A pipeline tool for analysis and detection of single nucleotide polymorphism (SNP) in 454 EST sequencing data. AASsites Description : A web-based pipeline for analysis of single nucleotide polymorphism (SNP) containing sequences to detect causes for altered splicing pattern. AbCD Description : A web tool that provides pre-estimated effective sample sizes, specific to each minor allele frequency (MAF) category, for designs with arbitrary coverage (0.5-30X) and sample size (20-20,000), and for four major ethnic groups (Europeans, Africans, Asians and African Americans). AD-LIBS Description : A local ancestry inference tool for low-coverage resequencing data. adegenet Description : An R package for analysis of large, genome-wide SNP data. ADMIXPIPE Description : ADMIXPIPE is a pipeline tool for integration of ADMIXTURE analysis with variant call format (VCF) filtering tools to generate file types that can be analyzed by CLUMPAK . Dependencies: PLINK 1.9 beta 4.5 or newer, VCFtools, Admixture ADMIXTURE Description : A tool to estimate individual ancestry from single nucleotide polymorphism (SNP) data sets. AffyMAPSDetector Description : A tool for annotation and characterization of SNP contributions to anomalous probe binding behavior. AffyPipe Description : A software tool combining all Affymetrix software. It also allows editing of SNP probe classes directly and to export genotypes in PLINK format. ALICE Description : an integrated analysis of allele frequency, allelic imbalance, loss of heterozygosity, long contiguous stretch of homozygosity, and copy number variation or alteration based on SNP probe hybridization intensities and genotypes. ALOHOMORA Description : Facilitates genome-wide linkage studies done with high-density single nucleotide polymorphism (SNP) marker panels, such as the Affymetrix GeneChip(R) Human Mapping 10K Array. Altools Description : Uses the BWA/SAMtools/VarScan pipeline to call SNPs and indels, and the dnaCopy algorithm for genome segmentation to identify copy number variations. Uses insert size information to detect large deletions. AMF, AgroMarker Finder Description : A tool for restriction site associated data (RAD) analysis for identification of polymorphism, SNPs and indels for rice genome. AncestrySNPminer Description : A web tool to retrieve and develop ancestry informative SNP panels. It also includes various population genomics statistical methods. AnnTools Description : A tool annotating single nucleotide substitutions (SNP/SNV), indels, and copy number variations (CNV) in sequencing and microarray data. argyle Description : An R package for analysis of genotyping Illumina array array data. ArrayFusion Description : A tool to annotate CGH results and microarray data from a range of platforms, such as cDNA, expression, exon, SNP, array-CGH and ChIP-on-chip. It converts the data into standard formats that can be visualized in Affymetrix Integrated Genome Browser and GBrowse in the HapMap Project. ARTS Description : A web-based tool for a set-up of high-throughput genome-wide mapping panels for the SNP genotyping of mouse mutants. ASSIsT Description : An automatic SNP scoring tool for in- and outbreeding species. Customized pipeline for calling and filtering of SNPs from Illumina Infinium arrays. ASSIsT builds on GenomeStudio-derived data and identifies markers that follow a bi-allelic genetic model and show reliable genotype calls, and re-edits SNP calls. AssociationViewer Description : A application to display single nucleotide polymorphism (SNP) in a genome. Atlas-SNP2 Description : A SNP discovery method to assess variant allele probability. atSNP Description : atSNP ( Affinity Test for regulatory SNP detection ) is a tool for computation of affinity scores single nucleotide polymorphism (SNP) and a reference. The atSNP algorithm computes p-values based on position weight matrices (PWMs). atSNP Search Description : atSNP Search is a web-based tool and database for analysis of human genome motifs with reference and variant alleles. The atSNP algorithm assesses and tests the variant alteration significance. atSNP also produces graphical representations of the motif matches. Currently, the database contains over 37 billion variant-motif pairs. AutoSNPa Description : A tool to graphically visualize Affymetrix single nucleotide polymorphism (SNP). BALL-SNP Description : A tool to identify candidate non-synonymous single nucleotide polymorphisms (SNPs) in a single protein by visualizing the mutated residues within the wild type structure. Based on the Biochemical Algorithms Library (BALL). BAM-matcher Description : A tool to determine if two separate BAM files contain reads sequenced from the same sample by counting genotype matches at SNPs. Bayenv Description : Software implementing a Bayesian method that uses a set of markers to estimate a pattern of covariance in allele frequencies between different populations. The estimation is used as a null model for testing individual SNPs. BGT Description : A command-line tool to store and query whole-genome genotypes. Bis-SNP Description : A package based on the Genome Analysis Toolkit (GATK) map-reduce framework for genotyping and DNA methylation calling in bisulfite treated massively parallel sequencing. Uses bayesian inference with locus specific methylation probabilities and bisulfite conversion rate of different cytosine contextto determine genotypes and methylation levels simultaneously.
Dear Inggriani, please check the following tools and software for your desired work.
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