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Found 50 result(s)

NCBI Epigenomics

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>>>!!! <<< The Epigenomics database was retired on June 1, 2016. All epigenomics data are available in our GEO resource https://www.ncbi.nlm.nih.gov/geo >>> !!! <<< The Epigenomics database provides genomics maps of stable and reprogrammable nuclear changes that control gene expression and influence health. Users can browse current epigenomic experiments as well as search, compare and browse samples from multiple biological sources in gene-specific contexts. Many epigenomes contain modifications with histone marks, DNA methylation and chromatin structure activity. NCBI Epigenomics database contains datasets from the NIH Roadmap Epigenomics Project.

DNA Data Bank of Japan

DDBJ

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DDBJ; DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.Since we exchange the collected data with EMBL-Bank/EBI; European Bioinformatics Institute and GenBank/NCBI; National Center for Biotechnology Information on a daily basis, the three data banks share virtually the same data at any given time. The virtually unified database is called "INSD; International Nucleotide Sequence Database DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession number to researchers in any other countries.

NCBI Reference Sequence Database

RefSeq

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The Reference Sequence (RefSeq) collection provides a comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins. RefSeq sequences form a foundation for medical, functional, and diversity studies. They provide a stable reference for genome annotation, gene identification and characterization, mutation and polymorphism analysis (especially RefSeqGene records), expression studies, and comparative analyses.

NCBI HomoloGene

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The HomoloGene database provides a system for the automated detection of homologs among annotated genes of genomes across multiple species. These homologs are fully documented and organized by homology group. HomoloGene processing uses proteins from input organisms to compare and sequence homologs, mapping back to corresponding DNA sequences.

The Arabidopsis Information Resource

TAIR

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The Arabidopsis Information Resource (TAIR) maintains a database of genetic and molecular biology data for the model higher plant Arabidopsis thaliana . Data available from TAIR includes the complete genome sequence along with gene structure, gene product information, metabolism, gene expression, DNA and seed stocks, genome maps, genetic and physical markers, publications, and information about the Arabidopsis research community. Gene product function data is updated every two weeks from the latest published research literature and community data submissions. Gene structures are updated 1-2 times per year using computational and manual methods as well as community submissions of new and updated genes. TAIR also provides extensive linkouts from our data pages to other Arabidopsis resources.

ENCODE

Encyclopedia of DNA Elements

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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.

GenBank

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GenBank® is a comprehensive database that contains publicly available nucleotide sequences for almost 260 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.

Ensembl

e!

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The Ensembl project produces genome databases for vertebrates and other eukaryotic species. Ensembl is a joint project between the European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Institute (WTSI) to develop a software system that produces and maintains automatic annotation on selected genomes.The Ensembl project was started in 1999, some years before the draft human genome was completed. Even at that early stage it was clear that manual annotation of 3 billion base pairs of sequence would not be able to offer researchers timely access to the latest data. The goal of Ensembl was therefore to automatically annotate the genome, integrate this annotation with other available biological data and make all this publicly available via the web. Since the website's launch in July 2000, many more genomes have been added to Ensembl and the range of available data has also expanded to include comparative genomics, variation and regulatory data. Ensembl is a joint project between European Bioinformatics Institute (EBI), an outstation of the European Molecular Biology Laboratory (EMBL), and the Wellcome Trust Sanger Institute (WTSI). Both institutes are located on the Wellcome Trust Genome Campus in Hinxton, south of the city of Cambridge, United Kingdom.

NCBI Trace Archive

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<<<!!!<<< This repository is no longer available. (Trace Archive is scheduled to retire on June 17, 2022) >>>!!!>>>

DOE Joint Genome Institute Genome Portal

US Department of Energy Joint Genome Institute Genome Web Portal

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The Department of Energy (DOE) Joint Genome Institute (JGI) is a national user facility with massive-scale DNA sequencing and analysis capabilities dedicated to advancing genomics for bioenergy and environmental applications. Beyond generating tens of trillions of DNA bases annually, the Institute develops and maintains data management systems and specialized analytical capabilities to manage and interpret complex genomic data sets, and to enable an expanding community of users around the world to analyze these data in different contexts over the web. The JGI Genome Portal provides a unified access point to all JGI genomic databases and analytical tools. A user can find all DOE JGI sequencing projects and their status, search for and download assemblies and annotations of sequenced genomes, and interactively explore those genomes and compare them with other sequenced microbes, fungi, plants or metagenomes using specialized systems tailored to each particular class of organisms. Databases: Genome Online Database (GOLD), Integrated Microbial Genomes (IGM), MycoCosm, Phytozome

DTU Bioinformatics

Center for Biological Sequence Analysis (formerly)

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<<<!!!<<< DTU Bioinformatics was closed on 31 December 2018 as part of a reorganization at DTU >>>!!!>>>

GENCODE

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GENCODE is a scientific project in genome research and part of the ENCODE (ENCyclopedia Of DNA Elements) scale-up project. The GENCODE consortium was initially formed as part of the pilot phase of the ENCODE project to identify and map all protein-coding genes within the ENCODE regions (approx. 1% of Human genome). Given the initial success of the project, GENCODE now aims to build an “Encyclopedia of genes and genes variants” by identifying all gene features in the human and mouse genome using a combination of computational analysis, manual annotation, and experimental validation, and annotating all evidence-based gene features in the entire human genome at a high accuracy.

EMBL-EBI

European Molecular Biology Laboratory - European Bioinformatics Institute

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The European Bioinformatics Institute (EBI) has a long-standing mission to collect, organise and make available databases for biomolecular science. It makes available a collection of databases along with tools to search, download and analyse their content. These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular interactions and pathways. Connected to these are linking and descriptive data resources such as protein motifs, ontologies and many others. In many of these efforts, the EBI is a European node in global data-sharing agreements involving, for example, the USA and Japan.

modENCODE

Model Organism ENCyclopedia of DNA Elements

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<<<!!!<<< As of 2023, support to maintain the www.modencode.org and intermine.modencode.org sites have been retired following the end of funding. To access data from the modENCODE project, or for questions regarding the data they make available, please visit these databases: Fly data: FlyBase: ModENCODE data at FlyBase: https://wiki.flybase.org/wiki/FlyBase:ModENCODE_data_at_FlyBase FlyBase: https://www.re3data.org/repository/r3d100010591 Worm data: WormBase https://www.re3data.org/repository/r3d100010424 Data, including modENCODE and modERN project data, is also available at the ENCODE Portal: https://www.re3data.org/repository/r3d100013051 (search metadata and view datasets for Drosophila and Caenorhabditis https://www.encodeproject.org/matrix/?type=Experiment&control_type!=*&status=released&replicates.library.biosample.donor.organism.scientific_name=Drosophila+melanogaster&replicates.library.biosample.donor.organism.scientific_name=Caenorhabditis+elegans&replicates.library.biosample.donor.organism.scientific_name=Drosophila+pseudoobscura&replicates.library.biosample.donor.organism.scientific_name=Drosophila+mojavensis). >>>!!!>>>

NCBI GSS

dbGSS

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<<<!!!<<< GSS sequences are now being merged into the NCBI Nucleotide database >>>!!!>>>

REBASE

The Restriction Enzyme Database

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The Restriction Enzyme Database is a collection of information about restriction enzymes, methylases, the microorganisms from which they have been isolated, recognition sequences, cleavage sites, methylation specificity, the commercial availability of the enzymes, and references - both published and unpublished observations (dating back to 1952). REBASE is updated daily and is constantly expanding.

database of Sequence Tagged Sites

dbSTS

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<<<!!!<<< The page is no longer available. This database was already retired, and on this page users could find information on how to search and use these sequences. dbSTS was an NCBI resource that contained sequence data for short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. >>>!!!>>>

Sequence Read Archive

SRA

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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.

Greengenes

The Greengenes Database

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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.

Genome Sequence Archive

GSA

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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.

NCBI Genome

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<<<!!!<<< 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.

NCBI dbMHC

Major histocompatibility Complex database

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<<<!!!<<< The repository is no longer available - Data previously on the site are now available at ftp://ftp.ncbi.nlm.nih.gov/pub/mhc/mhc/Final Archive. >>>!!!>>> The dbMHC database provides an open, publicly accessible platform for DNA and clinical data related to the human Major Histocompatibility Complex (MHC). The dbMHC provides access to human leukocyte antigen (HLA) sequences, HLA allele and haplotype frequencies, and clinical datasets.

NCBI Protein Clusters

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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

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<<<!!!<<< 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. >>>!!!>>>

European Nucleotide Archive

ENA

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The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature.