Filter
Reset all

Subjects

Content Types

Countries

AID systems

API

Data access

Data access restrictions

Database access

Database access restrictions

Database licenses

Data licenses

Data upload

Data upload restrictions

Enhanced publication

Institution responsibility type

Institution type

Keywords

Metadata standards

PID systems

Provider types

Quality management

Repository languages

Software

Syndications

Repository types

Versioning

  • * at the end of a keyword allows wildcard searches
  • " quotes can be used for searching phrases
  • + represents an AND search (default)
  • | represents an OR search
  • - represents a NOT operation
  • ( and ) implies priority
  • ~N after a word specifies the desired edit distance (fuzziness)
  • ~N after a phrase specifies the desired slop amount
Found 35 result(s)

Autism Chromosome Rearrangement Database

ACRD

Subject(s)
Content type(s)
Country
The Autism Chromosome Rearrangement Database is a collection of hand curated breakpoints and other genomic features, related to autism, taken from publicly available literature: databases and unpublished data. The database is continuously updated with information from in-house experimental data as well as data from published research studies.

Infevers

The registry of Auto-Inflammatory Disease mutations

Subject(s)
Content type(s)
Country
The ISSAID website gathers resources related to the systemic autoinflammatory diseases in order to facilitate contacts between interested physicians and researchers. The website provides support to share and rapidly disseminate information, thoughts, feelings and experiences to improve the quality of life of patients and families affected by systemic autoinflammatory diseases, and promote advances in the search for causes and cures.

NCBI Gene

Gene

Subject(s)
Content type(s)
Country
The Gene database provides detailed information for known and predicted genes defined by nucleotide sequence or map position. Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems.

ENCODE

Encyclopedia of DNA Elements

Subject(s)
Content type(s)
Country
The ENCODE Encyclopedia organizes the most salient analysis products into annotations, and provides tools to search and visualize them. The Encyclopedia has two levels of annotations: Integrative-level annotations integrate multiple types of experimental data and ground level annotations. Ground-level annotations are derived directly from the experimental data, typically produced by uniform processing pipelines.

NCBI Datasets

Subject(s)
Content type(s)
Country
NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

NCBI Protein Clusters

Subject(s)
Content type(s)
Country
The Entrez Protein Clusters database contains annotation information, publications, structures and analysis tools for related protein sequences encoded by complete genomes. The data available in the Protein Clusters Database is generated from prokaryotic genomic studies and is intended to assist researchers studying micro-organism evolution as well as other biological sciences. Available genomes include plants and viruses as well as organelles and microbial genomes.

NCBI Clone DB

NCBI clone registry

Subject(s)
Content type(s)
Country
<<<!!!<<< NCBI announced plans to retire the Clone DB web interface. Pursuant to this retirement, starting on May 27, 2019, all web pages associated with Clone DB and CloneFinder will redirect to this blog post https://ncbiinsights.ncbi.nlm.nih.gov/?s=clone+db. Links to Clone DB from the NCBI home page will also be going away. >>>!!!>>>

Ensembl Metazoa

e!EnsemblMetazoa

Subject(s)
Content type(s)
Country
Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.

Greengenes

The Greengenes Database

Subject(s)
Content type(s)
Country
Greengenes is an Earth Sciences website that assists clinical and environmental microbiologists from around the globe in classifying microorganisms from their local environments. A 16S rRNA gene database addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.

PeptideAtlas

Subject(s)
Content type(s)
Country
The PeptideAtlas validates expressed proteins to provide eukaryotic genome data. Peptide Atlas provides data to advance biological discoveries in humans. The PeptideAtlas accepts proteomic data from high-throughput processes and encourages data submission.

ChIP-Seq Transcription Factor Data

ChIP-Seq

Subject(s)
Content type(s)
Country
We developed a method, ChIP-sequencing (ChIP-seq), combining chromatin immunoprecipitation (ChIP) and massively parallel sequencing to identify mammalian DNA sequences bound by transcription factors in vivo. We used ChIP-seq to map STAT1 targets in interferon-gamma (IFN-gamma)-stimulated and unstimulated human HeLa S3 cells, and compared the method's performance to ChIP-PCR and to ChIP-chip for four chromosomes.For both Chromatin- immunoprecipation Transcription Factors and Histone modifications. Sequence files and the associated probability files are also provided.

Cancer GenomeAtlas Data Portal

Cancer Genome Atlas Data Portal

Subject(s)
Content type(s)
Country
The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The Data Coordinating Center (DCC) is the central provider of TCGA data. The DCC standardizes data formats and validates submitted data.

Brain Transcriptome Database

BrainTx

Subject(s)
Content type(s)
Country
The Brain Transcriptome Database (BrainTx) project aims to create an integrated platform to visualize and analyze our original transcriptome data and publicly accessible transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain.

JGI MycoCosm

MycoCosm - the fungal genomics resource

Subject(s)
Content type(s)
Country
MycoCosm, the DOE JGI’s web-based fungal genomics resource, which integrates fungal genomics data and analytical tools for fungal biologists. It provides navigation through sequenced genomes, genome analysis in context of comparative genomics and genome-centric view. MycoCosm promotes user community participation in data submission, annotation and analysis.

cisRED

Databases of genome-wide regulatory module and element predictions

Subject(s)
Content type(s)
Country
<<<!!!<<< This repository is no longer available. >>>!!!>>>

NCBI Genome

Subject(s)
Content type(s)
Country
<<<!!!<<< Effective May 2024, NCBI's Genome resource will no longer be available. NCBI Genome data can now be found on the NCBI Datasets taxonomy pages. https://www.re3data.org/repository/r3d100014298 >>>!!!>>> The Genome database contains annotations and analysis of eukaryotic and prokaryotic genomes, as well as tools that allow users to compare genomes and gene sequences from humans, microbes, plants, viruses and organelles. Users can browse by organism, and view genome maps and protein clusters.

Universal PBM Resource for Oligonucleotide Binding Evaluation

UniPROBE

Subject(s)
Content type(s)
Country
The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins. This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In total, the database currently hosts DNA binding data for 406 nonredundant proteins from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, mouse, and human. The database's web tools (on the right) include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences

International HapMap Project

国际人类基因组单体型图计划

Subject(s)
Content type(s)
Country
<<<!!!<<< OFFLINE >>>!!!>>> A recent computer security audit has revealed security flaws in the legacy HapMap site that require NCBI to take it down immediately. We regret the inconvenience, but we are required to do this. That said, NCBI was planning to decommission this site in the near future anyway (although not quite so suddenly), as the 1,000 genomes (1KG) project has established itself as a research standard for population genetics and genomics. NCBI has observed a decline in usage of the HapMap dataset and website with its available resources over the past five years and it has come to the end of its useful life. The International HapMap Project is a multi-country effort to identify and catalog genetic similarities and differences in human beings. Using the information in the HapMap, researchers will be able to find genes that affect health, disease, and individual responses to medications and environmental factors. The Project is a collaboration among scientists and funding agencies from Japan, the United Kingdom, Canada, China, Nigeria, and the United States. All of the information generated by the Project will be released into the public domain. The goal of the International HapMap Project is to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. By making this information freely available, the Project will help biomedical researchers find genes involved in disease and responses to therapeutic drugs. In the initial phase of the Project, genetic data are being gathered from four populations with African, Asian, and European ancestry. Ongoing interactions with members of these populations are addressing potential ethical issues and providing valuable experience in conducting research with identified populations. Public and private organizations in six countries are participating in the International HapMap Project. Data generated by the Project can be downloaded with minimal constraints. The Project officially started with a meeting in October 2002 (https://www.genome.gov/10005336/) and is expected to take about three years.

Addgene

Subject(s)
Content type(s)
Country
Addgene archives and distributes plasmids for researchers around the globe. They are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request.

CryptoDB

Subject(s)
Content type(s)
Country
CryptoDB is an integrated genomic and functional genomic database for the parasite Cryptosporidium and other related genera. CryptoDB integrates whole genome sequence and annotation along with experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining.

NCBI dbVar

Database of genomic structural VARiation

Subject(s)
Content type(s)
Country
The dbVar is a database of genomic structural variation containing data from multiple gene studies. Users can browse data containing the number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals. ***NCBI will phase out support for non-human organism data in dbSNP and dbVar beginning on September 1, 2017 ***

Estonian Biocentre Free Data

Subject(s)
Content type(s)
Country
A small genotype data repository containing data used in recent papers from the Estonian Biocentre. Most of the data pertains to human population genetics. PDF files of the papers are also freely available.

PhytoPath

Subject(s)
Content type(s)
Country
<<<!!!<<< This site is no longer maintained and is provided for reference only. Some functionality or links may not work. For all enquiries please contact the Ensembl Helpdesk http://www.ensembl.org/Help/Contact >>>!!!>>> PhytoPath is a new bioinformatics resource that integrates genome-scale data from important plant pathogen species with literature-curated information about the phenotypes of host infection. Using the Ensembl Genomes browser, it provides access to complete genome assembly and gene models of priority crop and model-fungal, oomycete and bacterial phytopathogens. PhytoPath also links genes to disease progression using data from the curated PHI-base resource. PhytoPath portal is a joint project bringing together Ensembl Genomes with PHI-base, a community-curated resource describing the role of genes in pathogenic infection. PhytoPath provides access to genomic and phentoypic data from fungal and oomycete plant pathogens, and has enabled a considerable increase in the coverage of phytopathogen genomes in Ensembl Fungi and Ensembl Protists. PhytoPath also provides enhanced searching of the PHI-base resource as well as the fungi and protists in Ensembl Genomes.

Ensembl Bacteria

e!EnsemblBacteria

Subject(s)
Content type(s)
Country
This site provides access to complete, annotated genomes from bacteria and archaea (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). Ensembl Bacteria contains genomes from annotated INSDC records that are loaded into Ensembl multi-species databases, using the INSDC annotation import pipeline.

Ensembl Protists

e!EnsemblProtists

Subject(s)
Content type(s)
Country
EnsemblProtists is a genome-centric portal for protists species.