Filter

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

Profiles

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 77 result(s)

Comparative RNA Web

CRW

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
Country
The Comparative RNA Web (CRW) Site disseminates information about RNA structure and evolution that has been determined using comparative sequence analysis. We present both raw (sequences, structure models, metadata) and processed (analyses, evolution, accuracy) data, organized into four main sections.

doRiNA

database of RNA interactions in post-transcriptional regulation

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
  • serviceProvider
Country
doRiNA is a database of transcriptome-wide binding site data for RNA binding proteins and microRNAs

RNA Abundance Database

RAD

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
Country
<<<!!!<<< This repository is no longer available. Due to changes in technology and funding, the RAD website is no longer available >>>!!!>>>

Sequence Read Archive

SRA

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
Country
The Sequence Read Archive stores the raw sequencing data from such sequencing platforms as the Roche 454 GS System, the Illumina Genome Analyzer, the Applied Biosystems SOLiD System, the Helicos Heliscope, and the Complete Genomics. It archives the sequencing data associated with RNA-Seq, ChIP-Seq, Genomic and Transcriptomic assemblies, and 16S ribosomal RNA data.

Nucleic Acid Knowledgebase

NAKB

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
  • serviceProvider
Country
NAKB provides Search, Report, Statistics, Atlas and Visualization for all nucleic-acid containing experimentally determined 3D structures held by NDB and by the Protein Data Bank (PDB), including all major methods: X-ray, Electron Microscopy, and NMR. For each structure, links are provided to external resources that annotate and analyze nucleic acid structures and their complexes.

Datanator

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
Country
Datanator is an integrated database of genomic and biochemical data designed to help investigators find data about specific molecules and reactions in specific organisms and specific environments for meta-analyses and mechanistic models. Datanator currently includes metabolite concentrations, RNA modifications and half-lives, protein abundances and modifications, and reaction kinetics integrated from several databases and numerous publications. The Datanator website and REST API provide tools for extracting clouds of data about specific molecules and reactions in specific organisms and specific environments, as well as data about similar molecules and reactions in taxonomically similar organisms.

NCBI Protein

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • serviceProvider
Country
The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.

SARS-CoV-2 Data Hub

SARS-CoV

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
  • serviceProvider
Country
This Web resource provides data and information relevant to SARS coronavirus. It includes links to the most recent sequence data and publications, to other SARS related resources, and a pre-computed alignment of genome sequences from various isolates. In order to provide free and easy access to genome and protein sequences and associated metadata from the SARS-CoV-2, we created a dedicated Severe acute respiratory syndrome coronavirus 2 data hub. You can access the Results Table on SARS-CoV-2 data hub, by pressing "RefSeq genomes", "nucleotide" or "protein" links on announcement banner located on NCBI home page, in "Find data" navigation menu or using "Up-to-date SARS-CoV-2" shortcut button in "Search by virus" form. SARS-CoV-2 sequences is part of NCBI Virus https://www.re3data.org/repository/r3d100014322

Genome Sequence Archive

GSA

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
  • serviceProvider
Country
GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing services free of charge for worldwide scientific communities. In addition to raw sequencing data, GSA also accommodates secondary analyzed files in acceptable formats (like BAM, VCF). Its user-friendly web interfaces simplify data entry and submitted data are roughly organized as two parts, viz., Metadata and File, where the former can be further assorted into BioProject, BioSample, Experiment and Run, and the latter contains raw sequence reads.

Mammalian Transcriptomic Database

MTD

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
Country
MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features.

Ensembl Bacteria

e!EnsemblBacteria

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
  • serviceProvider
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.

UniGene

Subject(s)
Repository type(s)
  • disciplinary
  • other
Provider type(s)
  • serviceProvider
Country
<<<!!!<<< This repository is no longer available>>>!!!>>>. Although the web pages are no longer available, you will still be able to download the final UniGene builds as static content from the FTP site https://ftp.ncbi.nlm.nih.gov/repository/UniGene/. You will also be able to match UniGene cluster numbers to Gene records by searching Gene with UniGene cluster numbers. For best results, restrict to the “UniGene Cluster Number” field rather than all fields in Gene. For example, a search with Mm.2108[UniGene Cluster Number] finds the mouse transthyretin Gene record (Ttr). You can use the advanced search page https://www.ncbi.nlm.nih.gov/gene/advanced to help construct these searches. Keep in mind that the Gene record contains selected Reference Sequences and GenBank mRNA sequences rather than the larger set of expressed sequences in the UniGene cluster.

National Genomics Data Center

国家基因组科学数据中心

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
  • serviceProvider
Country
The National Genomics Data Center (NGDC), part of the China National Center for Bioinformation (CNCB), advances life & health sciences by providing open access to a suite of resources, with the aim to translate big data into big discoveries and support worldwide activities in both academia and industry.

MozAtlas

Subject(s)
Repository type(s)
  • institutional
  • disciplinary
Provider type(s)
  • serviceProvider
  • dataProvider
Country
MozAtlas provides gene expression data of adult male and female mosquitoes as tables, expressions, trees and models. MozAtlas also provides sequence orthology relationships with data provided by FlyBase, Vectorbase, Beetlebase, BeeBase, and WormBase.

MicrosporidiaDB

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
Country
MicrosporidiaDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the phylum Microsporidia. In its first iteration (released in early 2010), MicrosporidiaDB contains the genomes of two Encephalitozoon species (see below). MicrosporidiaDB integrates whole genome sequence and annotation and will rapidly expand to include experimental data and environmental isolate sequences provided by community researchers. The database includes supplemental bioinformatics analyses and a web interface for data-mining.

Expressed Sequence Tags database

dbEST

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
Country
dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. Expressed Sequence Tags (ESTs) are short (usually about 300-500 bp), single-pass sequence reads from mRNA (cDNA). Typically they are produced in large batches. They represent a snapshot of genes expressed in a given tissue and/or at a given developmental stage. They are tags (some coding, others not) of expression for a given cDNA library. Most EST projects develop large numbers of sequences. These are commonly submitted to GenBank and dbEST as batches of dozens to thousands of entries, with a great deal of redundancy in the citation, submitter and library information. To improve the efficiency of the submission process for this type of data, we have designed a special streamlined submission process and data format. dbEST also includes sequences that are longer than the traditional ESTs, or are produced as single sequences or in small batches. Among these sequences are products of differential display experiments and RACE experiments. The thing that these sequences have in common with traditional ESTs, regardless of length, quality, or quantity, is that there is little information that can be annotated in the record. If a sequence is later characterized and annotated with biological features such as a coding region, 5'UTR, or 3'UTR, it should be submitted through the regular GenBank submissions procedure (via BankIt or Sequin), even if part of the sequence is already in dbEST. dbEST is reserved for single-pass reads. Assembled sequences should not be submitted to dbEST. GenBank will accept assembled EST submissions for the forthcoming TSA (Transcriptome Shotgun Assembly) division. The individual reads which make up the assembly should be submitted to dbEST, the Trace archive or the Short Read Archive (SRA) prior to the submission of the assemblies.

Cancer GenomeAtlas Data Portal

Cancer Genome Atlas Data Portal

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
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.

Ensembl Fungi

e!EnsemblFungi

Subject(s)
Repository type(s)
  • disciplinary
  • institutional
Provider type(s)
  • dataProvider
  • serviceProvider
Country
EnsemblFungi is a genome-centric portal for fungal species. It is a project to maintain annotation on selected genomes.

Nucleic Acid Database

NDB

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
Country
<<<!!!<<<This repository is offline>>>!!!>>> The NDB is a resource for nucleic acid research and education. The NDB assembles and distributes information about the three-dimensional structures of nucleic acids through a variety of resources, including a searchable database, Atlas, and software.

SILVA

A comprehensive on-line resource for quality checked and aligned ribosomal RNA sequence data.

Subject(s)
Repository type(s)
  • disciplinary
  • institutional
Provider type(s)
  • serviceProvider
Country
SILVA is a comprehensive, quality-controlled web resource for up-to-date aligned ribosomal RNA (rRNA) gene sequences from the Bacteria, Archaea and Eukaryota domains alongside supplementary online services. In addition to data products, SILVA provides various online tools such as alignment and classification, phylogenetic tree calculation and viewer, probe/primer matching, and an amplicon analysis pipeline. With every full release a curated guide tree is provided that contains the latest taxonomy and nomenclature based on multiple references. SILVA is an ELIXIR Core Data Resource.

Ensembl Plants

e!EnsemblPlants

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • serviceProvider
  • dataProvider
Country
EnsemblPlants is a genome-centric portal for plant species. Ensembl Plants is developed in coordination with other plant genomics and bioinformatics groups via the EBI's role in the transPLANT consortium.

SimTK

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
Country
SimTK is a free project-hosting platform for the biomedical computation community that enables researchers to easily share their software, data, and models and provides the infrastructure so they can support and grow a community around their projects. It has over 126.656 members, hosts 1.648 projects from researchers around the world, and has had more than 2.095.783 files downloaded from it. Individuals have created SimTK projects to meet publisher and funding agencies’ software and data sharing requirements, run scientific challenges, create a collection of their community’s resources, and much more.

Ensembl Metazoa

e!EnsemblMetazoa

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
  • serviceProvider
Country
Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.

Integrated Resource for Reproducibility in Macromolecular Crystallography

IRRMC

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
Country
The Integrated Resource for Reproducibility in Macromolecular Crystallography includes a repository system and website designed to make the raw data of protein crystallography more widely available. Our focus is on identifying, cataloging and providing the metadata related to datasets, which could be used to reprocess the original diffraction data. The intent behind this project is to make the resulting three dimensional structures more reproducible and easier to modify and improve as processing methods advance.

The Human Protein Atlas

HPA

Subject(s)
Repository type(s)
  • disciplinary
Provider type(s)
  • dataProvider
  • serviceProvider
Country
The Swedish Human Protein Atlas project has been set up to allow for a systematic exploration of the human proteome using Antibody-Based Proteomics. This is accomplished by combining high-throughput generation of affinity-purified antibodies with protein profiling in a multitude of tissues and cells assembled in tissue microarrays. Confocal microscopy analysis using human cell lines is performed for more detailed protein localization. The program hosts the Human Protein Atlas portal with expression profiles of human proteins in tissues and cells. The main objective of the resource centre is to produce specific antibodies to human target proteins using a high-throughput production method involving the cloning and protein expression of Protein Epitope Signature Tags (PrESTs). After purification, the antibodies are used to study expression profiles in cells and tissues and for functional analysis of the corresponding proteins in a wide range of platforms.