Tag: genetic variation

The International Genome Sample Resource (IGSR) was established to ensure the ongoing usability of data generated by the 1000 Genomes Project and to extend the data set. The 1000 Genomes Project ran between 2008 and 2015, creating the largest public ...

MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease. Data includes gene characterization, nomenclature, mapping, gene homo ...

The Catalogue of Somatic Mutations in Cancer (COSMIC) is a database of manually-curated somatic mutation information relating to human cancers. The COSMIC database combines manually-curated data and genome-wide screen data.

DisGeNET is a discovery platform containing one of the largest collections available of genes and variants involved in human diseases. DisGeNET integrates data from expert curated repositories, GWAS catalogues, animal models, and the scientific liter ...

The European Variation Archive is an open-access archive that accepts submission of, and provides access to, all types of genetic variation data from all species. All users are able to download any dataset, or query our study catalogue via our variat ...

Online Mendelian Inheritance in Man. It is an authoritative compendium of human genes and phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 15,000 genes. OMIM focuses on the relation ...

Genome Aggregation Database (gnomAD) - browser that aggregates exome and whole-genome sequencing data from a wide variety of large-scale sequencing projects. It enables search of genetic variation information by gene, variant or region.

The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.

ClinVar is a freely accessible, public archive of reports of the relationships among human variations and phenotypes, with supporting evidence. ClinVar thus facilitates access to and communication about the relationships asserted between human variat ...

Genotype-Tissue Expression (GTEx) - database which helps to study the relationship between genetic variation and gene expression in human tissues.

BRCA Share is a novel gene datashare initiative that provides scientists and commercial laboratory organizations around the world with open access to BRCA Share (formerly UMD-BRCA1) contains BRCA1 and BRCA2 genetic data. The program’s goal is to acce ...

dbVar is a database of human genomic structural variation where users can search, view, and download data from submitted studies. dbVar stopped supporting data from non-human organisms in 2017, however existing non-human data remains available. In ke ...

The Stanford HIV Drug Resistance Database (HIVDB) is an essential resource for public health officials monitoring ADR and TDR, for scientists developing new ARV drugs, and for HIV care providers managing patients with HIVDR.

T-DNA insertions in Arabidopsis and their flanking sequence tags.

The Leiden Open Variation Database (LOVD) provides a flexible, freely available tool for gene-centered collection and display of DNA variations. LOVD also stores patient-centered data, NGS data, and variants outside of genes.

The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database providing centralized access to Rosaceae genomics and genetics data and analysis tools to facilitate cross-species utilization of data.

The Allele Frequency Net Database (AFND) provides the scientific community with a freely available repository for the storage of frequency data (alleles, genes, haplotypes and genotypes) related to human leukocyte antigens (HLA), killer-cell immunogl ...

H-Invitational Database (H-InvDB) is an integrated database of human genes and transcripts. By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splici ...

The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-ref ...

PhenoM (Phenomics of yeast Mutants) stores, retrieves, visualises and data mines the quantitative single-cell measurements extracted from micrographs of temperature-sensitive mutant cells. PhenoM allows users to rapidly search and retrieve raw images ...

The Human Gene Mutation Database (HGMD) - comprehensive collection of germline mutations in nuclear genes that underlie, or are associated with, human inherited disease. It is a flexible resource that can be adapted to a broad range of applications i ...

PolymiRTS (Polymorphism in microRNAs and their TargetSites) is a database of naturally occurring DNA variations in microRNA (miRNA) seed regions and miRNA target sites. MicroRNAs pair to the transcripts of protein-coding genes and cause translational ...

The Exome Aggregation Consortium (ExAC) is a coalition of investigators seeking to aggregate and harmonize exome sequencing data from a variety of large-scale sequencing projects, and to make summary data available for the wider scientific community. ...

Zfishbook is a real-time database of transposon-labeled mutants in zebrafish. This resource provides services for any size of GBT mutagenesis projects on zebrafish to encourage collaboration in the research community.

AmoebaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for Entamoeba and Acanthamoeba parasites. In its first released, AmoebaDB contained the genomes of three Entamoeba species. AmoebaDB int ...

SNPedia is a wiki resource of the functional consequences of human genetic variation as published in peer-reviewed studies. Entries are formatted to allow associations to be assigned to single genotypes as well as sets of genotypes (genosets). Curati ...

Method to assess the outcome of non-synonymous SNVs using a CONsensus DELeteriousness score that combines various tools.

Database developed for functional prediction and annotation of all potential non-synonymous single-nucleotide variants (nsSNVs) and splice-site variants (ssSNVs) in the human genome. It also facilitates the steps of filtering and prioritizing SNVs fr ...

The Network of Cancer Genes (NCG) contains information on duplicability, evolution, protein-protein and microRNA-gene interaction, function, expression and essentiality of cancer genes from manually curated publications . NCG also provides informatio ...

The International Cancer Genome Consortium (ICGC) is a collaborative effort to characterize genomic abnormalities in 50 different cancer types. Currently has data from 24 cancer projects. Open access data (eg. Somatic mutations, copy number alteratio ...

The Immuno Polymorphism Database (IPD) is a set of specialist databases related to the study of polymorphic genes in the immune system. IPD currently consists of four databases: IPD-KIR, contains the allelic sequences of Killer-cell Immunoglobulin-li ...

The ITHANET Portal represents an expanding resource for clinicians and researchers dealing with haemoglobinopathies and a port of call for patients in search of professional advice. The ITHANET Portal integrates information on news, events, clinical ...

The Bovine Genome Database project is developed to support the efforts of bovine genomics researchers by providing data mining, genome navigation and annotation tools for the bovine reference genome based on the hereford cow, L1 Dominette 01449.

The goal of MutDB is to annotate human variation data with protein structural information and other functionally relevant information, if available. The mutations are organized by gene. Click on the alphabet below to go alphabetically through the lis ...

Families of nuclear hormone receptors

COVDB contains cell culture, animal model, and clinical data on compounds with a proven or potential anti-coronavirus activity.

Cytochrome P450 alleles and drug interactions

Polymorphic miRNA-mediated gene regulation in vertebrates

Provides a searchable repository of highly curated HLA sequences. The naming of these HLA genes and alleles and their quality control is the responsibility of the WHO Nomenclature Committee for Factors of the HLA System. Through the work of the HLA I ...

DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance.

The Selective Targets database (SelTarbase ) is a curated database of public MNR mutation data in microsatellite unstable human tumors. A comprehensive database of all human coding, untranslated, non-coding RNA- and intronic MNRs (MNR_ensembl) is als ...

A global search engine for genetic mutations.

Universal Mutation Database (UMD) is a database for mutations. UMD-predictor is a tool that enables functional annotation of variants to find the relevant ones.

Blood Group Antigen Gene Mutation Database

non-B DNA forming motifs in mammalian genomes

DNA repair pathways of human, yeast and E.coli

PGG.SNV is database for understanding the evolutionary and medical implications of human single nucleotide variation (SNV) on a population level. It documents more than 300,000 genomes and 10 billion allele frequencies records for diverse human ethni ...

Database of Aberrant Splice Sites: sequences flanking cryptic and de novo 3' and 5' splice sites

Polymorphic inversions in the human genome

Repository for clinicians and scientists working in the rare disorder community. It enables secure sharing of case records by clinicians and rare disease scientists and helps the user to find additional cases of the same unnamed disorder. The reposit ...

Plant microRNA knowledge base

Attempt to summarize all known sequence variations in the human genome, to facilitate research into how genotypes affect common diseases, drug responses, and other complex phenotypes.

Indian Genetic Disease Database

DriverDB, a database that incorporates >9500 cancer-related RNA-seq datasets and >7000 more exome-seq datasets, in addition to annotation databases and published bioinformatics algorithms dedicated to driver gene/mutation identification. Seven additi ...

Autosomal monoallelic expression (MAE) refers to mitotically stable, epigenetically controlled allele-specific expression of autosomal genes, with the initial non-predetermined ('random') choice of thetranscriptional activity of the two alleles maint ...

A database of phosphorylation-related SNP (phosSNP) which are non-synonymous SNP (nsSNP) that affect the protein phosphorylation status. Using an in-house developed kinase-specific phosphorylation site predictor (GPS 2.0), we computationally detected ...

Cancer SNP data on copy number alterations

GWAS prioritization tool

Mouse Indel Polymorphism Database

NHLBI Exome Sequencing Project (ESP): Exome Variant Server (EVS) for browsing single nucleotide variation data from exome sequencing experiments mainly focused on heart, lung and blood disorders.

Linking RNA splicing and disease. Database that collects and curates data of RNA Splicing mutation and disease. The RNA Splicing mutations include cis-acting mutations that disrupt splicing and trans-acting mutations that affecting RNA-dependent func ...

Satellog is a database that catalogs all pure 1-16 repeat unit satellite repeats in the human genome along with supplementary data. Satellog analyzes each pure repeat in UniGene clusters for evidence of repeat polymorphism.

Mutant mouse lines held at MRC Harwell

Emory Genetics Laboratory's (EGL) Variant Classification Catalog contains variants of the gene of interest that has been seen and analysed by EGL Genetics.

Phenotypic data for Arabidopsis thaliana

FINDbase (http://www.findbase.org) is a relational database, derived from the ETHNOS software, recording frequencies of causative mutations leading to inherited disorders worldwide. Database records include the population and ethnic group, the disord ...

TFBSshape provides DNA shape features for transcription factor binding sites (TFBSs) that in addtion to sequence features, usually in the form of position weight matrices (PWMs), characterize DNA binding specificities of transcription factors (TFs) f ...

Genetic mutation database for rare diseases that enables to search, sort and filter genetic variants from clinically diagnosed individuals worldwide and make symptoms-based queries.

Visualize the natural connections between DNA sequences, natural variation (polymorphisms), molecular structures, protein-protein interactions, and gene expression patterns by combining several data visualization tools with a zoomable user interface.

Polymorphic Simple Sequence Repeats Database

Databases for genetic resources and plant disease information

> CORRECT NAME OF TOOL COULD ALSO BE 'TreeshrewDB v2.0' | Chromosomal level assembly and population sequencing of the Chinese tree shrew genome | Symbol Accession number Full gene name | &nbspFan Y, Yu D et al., 2014. Tree shrew database (TreeshrewDB ...

OGRDB is a curated database of immunoglobulin and T cell receptor sequences inferred from immune receptor repertoires, together with supporting information describing the repertoires from which they were derived. Researchers can submit sequences and ...

A system of databases documenting the influence of mutations in regulatory gene regions.

The duplicated gene nucleotide variants database (dbDNV) (http://goods.ibms.sinica.edu.tw/DNVs/) promotes accurate variation annotation. Aside from the flat file download, users can explore the gene-related duplications and the associated DNVs by DGL ...

PhenoModifier is a genetic modifier database for elucidating the genetic basis of human phenotypic variation. PhenoModifier provides a more complete spectrum of genetic factors contributing to human phenotypic variation and the portal has a broad sci ...

A comprehensive database of genomic variations that disturb ceRNA network regulation. Genomic VA,T,C,G RIATION disturbing ceRNA regulations. LnCeVar is a comprehensive database that aims to infer genomic variations that disturb lncRNA-associated ce ...

dbMTS is a comprehensive database of putative human microRNA target site (MTS) SNVs and their functional predictions. dbMTS collects all potential SNVs microRNA target seed regions in human 3’UTRs and provides their functional predictions and annotat ...

An open-source platform to distribute and interpret data from multiplexed assays of variant effect. Table of Multiplexed Assay of Variant Effect (MAVE) studies. MaveDB - A repository for MAVE assay datasets. To cite this document, please use the c ...

Gephebase is a manually-curated database compiling our accumulated knowledge of the genes and mutations that underlie natural, domesticated and experimental phenotypic variation in all Eukaryotes — mostly animals, plants and yeasts. Gephebase conso ...

Protein stability data

Consolidated database containing information on diseases, related genes and genetic variations, protein structures and drug information. The database is a useful platform for researchers studying the underlying mechanism for association among genetic ...

a database of carbohydrate-binding proteins. An open access database ready to answer your sweetest queries. Carbohydrate-binding proteins play crucial roles across all viruses and organisms

BEable-GPS: Base Editable prediction of Global Pathogenic-related SNVs. Comparison of cytosine base editors and development of the BEable-GPS database for targeting pathogenic SNVs.

Functional annotation of exon skipping event in human. Exon skipping (ES), the most common alternative splicing event, has been reported to contribute to diverse human diseases due to the loss of functional domains sites or frame shifting of open re ...

an adaptive immune receptor genotype and haplotype database. The adaptive immune receptor Genotype and Haplotype database. 11-Oct-2019 *NEW* - VDJbase is described in Nucleic Acids Research. VDJbase is a publicly available database that offers eas ...

an integrated database and analytic platform for de novo mutations in humans. De novo mutations (DNMs) significantly contribute to sporadic diseases, particularly in neuropsychiatric disorders. Whole-exome sequencing (WES) and whole-genome sequencin ...

Tool for the Unified Management of Clinical Information and Genetic Variants to Accelerate Variant Pathogenicity Classification.

Inherited glycophosphatidylinositol deficiency variant database.

LORD (linking opendata for rare diseases) - tool for browsing information about rare diseases. It aggregates the information from Orphanet, HPO and OMIM database.

a curated database for intrapatient tumor heterogeneity. CancerTracer is a manually curated and integrated database aims to help researchers to decipher tumor heterogeneity at individual patient level. It contains two types of tumor heterogeneity da ...

A database-integration approach for protein/genome information retrieval.

Data integration platform for molecular and clinical epidemiological analysis of tuberculosis.

An immunoinformatic database of T-cell-defined neoantigens. Interior-Design-Responsive-Website-Templates-Edge. NeoPeptide is a catalog of epitopes derived from neoantigens, arising from somatic mutations, captured from the literatures and immunolog ...

A curated knowledgebase on the proteins that are involved in the blood coagulation pathway. It contains information on sequence, accession number, source, taxonomy, keywords, function, subcellular location, tissue specificity, associated diseases, mu ...

CHG is a systematically integrated database of cancer hallmark genes. The database focuses on integrating hallmark genes in a systematic, standard way and annotates the potential roles of the hallmark genes in cancer processes.

Database for hotspot mutations and annotations in cancer. Hotspots, recurrently mutated DNA positions in cancer, are thought to be oncogenic drivers because random chance is unlikely and the knowledge of clear examples of oncogenic hotspots in genes ...

Integrated database of genome annotation, genomic diversity, and CAPS marker information for mandarin molecular breeding.

Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma.

A Comprehensive Hepatitis D Virus Database. Welcome to Hepatitis Delta Virus Database (HDVdb). The Hepatitis D Virus (HDV) Database, HDVdb contains comprehensive data on HDV genetic sequences that allows the researchers to investigate the genetic v ...

A database of cancer associated enhancers. A comprehensive resource on enhancer information for TCGA cancer types. CancerEnD Genome-wide association studies have successfully identified thousands of genomic loci potentially associated with hundreds ...

A database of global evaluation of SARS-CoV-2/hCoV-19 sequences. If you used GESS for scientific publication, we would appreciate citations to the following paper:.

It is a a joint ISA-CNR/UniSA project: a database in which information are collected and freely available about structural features of the enzymes involved in the galactose metabolism, i.e. galactose-1-phosphate uridylyltransferase (GALT, E.C. 2.7.7. ...

Variants of DNA mismatch repair genes derived from 33,998 Chinese individuals with and without cancer reveal their highly ethnic-specific nature. An open-access database of DNA mismatch repair (MMR) gene variants in Chinese population. DNA mismatch ...

Database for membrane protein thermodynamics for understanding folding and stability. MPTherm is a thermodynamic database of membrane proteins and their mutants, contains the thermodynamic data of membrane proteins collected from literature and ProT ...

CNAdbCC is a curated database for copy number aberrations analysis and visualization of cervical cancer. Currently, the database contains about 1,000 dataset samples mainly integrated by affymetrix and aligent platform. Affymetrix is based on light-c ...

An Integrative De Novo Variant Knowledge Base for Developmental Disorders. NeuroPsychiatric Mutation Knowledge Base. Welcome to our open access database PsyMuKB. PsyMuKB is a comprehensive knowledge base that links transcriptional and translationa ...

The availability of genetic variants, together with phenotypic annotations from model organisms, facilitates comparing these variants with equivalent variants in humans. However, existing databases and search tools do not make it easy to scan for equ ...

Interactions between HIV-1 and human proteins

Integration of Human and Model Organism Genetic Resources to Facilitate Functional Annotation of the Human Genome.

A search engine for human genomic variants.

Database platform for managing molecular data (sequence variants and DNA array) with associated phenotypes and analyzing the data for QTL mapping.

Diagnostic Variant Database (DVD) is a nation-wide human genomic variant database launched by Dutch University Medical Centers. Its purpose is to share all genetic variants detected in the course of next-generation sequencing (NGS) applications betwe ...

CHDGKB (A knowledgebase of non-syndromic congenital heart disease genetic variations) is a manually curated database of genetic variations associated with non syndromic congenital heart disease. CHDGKB contains a comprehensive information of genetic ...

Database of human missense variants mapped to 3D protein structures.

A database for predicting pathogenicity of missense sequence variants of keratin genes associated with genodermatoses.

A unified and manually curated repertoire of GRIN variants. A CURATED DATABASE FOR GRIN VARIANTS.

Software that includes powerful bioinformatics applications for genetic analysis and offers a comprehensive solution to the tasks of genomic variants annotation, filtration, interpretation and reporting. It includes Alamut Batch, which is a high-thro ...

FLHdb is database of variants of Familial Hemophagocytic Lymphohistiocytosis from the Clinical and Translational Bioinformatics Research Group at Vall Hebron Institute of Research (VHIR).

The Cystic Fibrosis Mutation Database (CFTR1) was initiated by the Cystic Fibrosis Genetic Analysis Consortium in 1989 to increase and facilitate communications among CF researchers, and is maintained by the Cystic Fibrosis Centre at the Hospital for ...

Domestic Animal Diversity Information System is a communication and information tool for implementing strategies for the management of animal genetic resources. It provides the user with searchable databases of breed-related information and images, m ...

Chlamydia trachomatis multilocus sequence typing (MLST) database.

Provides simple-to-use REST web services to query/retrieve variant annotation data, aggregated from many popular data resources.

CoV-Seq is a suite of tools and datasets for analysis and visualization of genomes of SARS-CoV-2, the virus that causes COVID-19. Sequences are collected from four major repositories: GISAID, NCBI, EMBL and CNGB.

A database for improving the rational design of glucose-tolerant β-glucosidases. A database of mutant β-glucosidases. Glutantbase is a database, webtool and method to evaluate mutations for β-glucosidases proteins used in industrial applications. G ...

FABRIC Cancer Portal is a comprehensive catalogue of human coding genes in cancer based on the FABRIC framework. FABRIC quantifies the selection of genes in tumor and weighs their evidence for being cancer drivers.

A Database of Curated Antibody Repertoires for Exploring antibody diversity and Predicting Antibody Prevalence | cAb-Rep is a database of curated antibody repertoires. It currently includes 306 B cell repertoires collected from 121 human individuals, ...