Tag: genomics

The Gene Ontology resource provides a computational representation of our current scientific knowledge about the functions of genes (or, more properly, the protein and non-coding RNA molecules produced by genes) from many different organisms, from hu ...

Ensembl aims to provide a centralized resource for geneticists, molecular biologists and other researchers studying the genomes of our own species and other vertebrates and model organisms. Ensembl is one of several well known genome browsers for the ...

Genome assemblies and aligned annotations for a wide range of vertebrates and model organisms, along with an integrated tool set for visualizing, comparing, analyzing and sharing both publicly available and user-generated genomic datasets.

Medical Subject Headings is the National Library of Medicine - controlled vocabulary used for indexing articles for PubMed and other NLM databases.

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 ...

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 provide ...

The Human Phenotype Ontology (HPO) provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being develope ...

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.

The European Genome-phenome Archive (EGA) allows you to explore datasets from genomic studies, provided by a range of data providers. Access to datasets must be approved by the specified Data Access Committee (DAC).

The NCBI Taxonomy is a database of taxonomic information. It does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based ...

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-co ...

The UCSC Archaeal Genome Browser is a window on the biology of more than 100 microbial species from the domain Archaea. Basic gene annotation is derived from NCBI Genbank/RefSeq entries, with overlays of sequence conservation across multiple species, ...

Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs contai ...

ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Expe ...

The Disease Ontology has been developed as a standardized ontology for human disease with the purpose of providing descriptions of human disease terms, phenotype characteristics and related medical vocabulary disease concepts. Releases: https://githu ...

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 ...

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relations ...

The Influenza Research Database (IRD) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated ...

modMine is an integrated web resource of data and tools to browse and search modENCODE data and experimental details, download results and access the GBrowse genome browser.

HGNC is responsible for approving unique symbols and names for human loci, including protein coding genes, ncRNA genes and pseudogenes, to allow unambiguous scientific communication.

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.

WormBase is an international consortium of biologists and computer scientists dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans and related nematod ...

The MEROPS database is an information resource for peptidases (also termed proteases, proteinases and proteolytic enzymes) and the proteins that inhibit them.

VectorBase is a web-accessible data repository for information about invertebrate vectors of human pathogens. VectorBase annotates and maintains vector genomes (as well as a number of non-vector genomes for comparative analysis) providing an integrat ...

Gramene's purpose is to provide added value to plant genomics data sets available within the public sector, which will facilitate researchers' ability to understand the plant genomes and take advantage of genomic sequence known in one species for ide ...

The Cancer Genome Atlas (TCGA) is a comprehensive, collaborative effort led by the National Institutes of Health (NIH) to map the genomic changes associated with specific types of tumors to improve the prevention, diagnosis and treatment of cancer. I ...

The Expression Atlas is a free resource providing information on gene expression patterns under different biological conditions in a variety of species. Gene expression data is re-analysed in-house to detect genes showing interesting baseline and dif ...

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.

The Zebrafish Information Network, ZFIN, serves as the primary community database resource for the laboratory use of zebrafish. We develop and support integrated zebrafish genetic, genomic, developmental and physiological information and link this in ...

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 pro ...

The Entrez Global Query Cross-Database Search System is a federated search engine, or web portal that allows users to search many discrete health sciences databases at the National Center for Biotechnology Information (NCBI) website. Entrez can effic ...

eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) is a database of orthologous groups of genes. The orthologous groups are annotated with functional description lines (derived by identifying a common denominator for the gene ...

JASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six taxo ...

The Ensembl genome annotation system, developed jointly by EMBL-EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented b ...

Phytozome, the Plant Comparative Genomics portal of the Department of Energy's Joint Genome Institute, provides JGI users and the broader plant science community a hub for accessing, visualizing and analyzing JGI-sequenced plant genomes, as well as s ...

The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Center ...

GeneCards is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes.

MetaCyc is the largest curated collection of metabolic pathways currently available. It provides a comprehensive resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecu ...

Pathway Commons is a convenient point of access to biological pathway information collected from public pathway databases. Information is sourced from public pathway databases and is readily searched, visualized, and downloaded. The data is freely av ...

The Rat Genome Database stores genetic, genomic, phenotype, and disease data generated from rat research. It provides access to corresponding data for eight other species, allowing cross-species comparison. Data curation is performed both manually an ...

Swiss Institute of Bioinformatics (SIB) coordinates research and education in bioinformatics throughout Switzerland and provides bioinformatics services to the national and international research community. ExPASy gives access to numerous repositorie ...

The Integrated Microbial Genomes (IMG/M) aims to support the annotation, analysis and distribution of microbial genome and microbiome datasets sequenced at DOE's Joint Genome Institute (JGI). It also serves as a community resource for analysis and an ...

Protein Ontology (PRO) provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them. Each PRO term represents a distinct class of entities (including specific modified forms ...

BMRB collects, annotates, archives, and disseminates (worldwide in the public domain) the important spectral and quantitative data derived from NMR spectroscopic investigations of biological macromolecules and metabolites. The goal is to empower scie ...

EBI Metagenomics has changed its name to MGnify to reflect a change in scope. This is a free-to-use resource aiming at supporting all metagenomics researchers. The service is an automated pipeline for the analysis and archiving of metagenomic data th ...

This database provides a list of insertion sequences (IS) isolated from bacteria and archae. It is organized into individual files containing their general features (name, size, origin, family.....) as well as their DNA and potential protein sequence ...

The Genomes Online Database provides access to information regarding genome and metagenome sequencing projects, and their associated metadata, around the world. Information in GOLD is organized into four levels: Study, Biosample/Organism, Sequencing ...

PHI-Base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. PHI-base catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete ...

ViralZone is a web resource for viral genes and families, providing detailed molecular and epidemiological information, along with virion and genome figures. Each virus or family page gives easy access to UniProtKB/Swiss-Prot viral protein entries.

BridgeDb is a framework and data repository for finding and mapping equivalent identifiers from various databases. BridgeDb provides a framework, live services, and identifier mapping files for genes, gene-variant, proteins, metabolites and interacti ...

The GO Annotation Database (GOA) provides Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB), RNA molecules from RNACentral and protein complexes from the Complex Portal. GOA files contain a mixture of manual annotati ...

BiGG Models is a knowledgebase of genome-scale metabolic network reconstructions. BiGG Models integrates more than 70 published genome-scale metabolic networks into a single database with a set of standardized identifiers called BiGG IDs.

DRSC Functional Genomics Resources (DRSC-FGR) began as the Drosophila RNAi Screening Center (DRSC), founded by Prof. Norbert Perrimon in 2003, and the Transgenic RNAi Project (TRiP), founded by Prof. Perrimon in 2008. DRSC-FGR has been previously kno ...

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 ...

PomBase is a model organism database that provides organization of and access to scientific data for the fission yeast Schizosaccharomyces pombe. PomBase supports genomic sequence and features, genome-wide datasets and manual literature curation as w ...

PATRIC is part of the Bacterial Bioinformatics Resource Center, and is an information system designed to support the biomedical research community’s work on bacterial infectious diseases via integration of vital pathogen information with rich data an ...

A structured controlled vocabulary for the source of an enzyme. It comprises terms for tissues, cell lines, cell types and cell cultures from uni- and multicellular organisms.

The BioSamples database aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRIDE. It provides lin ...

Ensembl Metazoa provides access to genomes of metazoans of interest in disease, environmental sciences, agriculture and economic concern. Extensive coverage exists of diptera, nematodes, lepidoptera and hymenoptera.

Ensembl Protists stores protist genomes of interest, covering those involved in disease and of scientific interest. This includes genomes such as Plasmodium falciparum, Dictyostelium discoideum, Phytophthora infestans and Leishmania major. A majority ...

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.

VFDB is an integrated and comprehensive database of virulence factors for bacterial pathogens (also including Chlamydia and Mycoplasma).

The Eukaryotic Promoter Database (EPD) provides accurate transcription start site (TSS) information for promoters of 15 model organisms, from human to yeast to the malaria parasite Plasmodium falciparum. While the original database was a manually cur ...

VIPERdb is a database for icosahedral virus capsid structures. The emphasis is on providing data from structural and computational analyses on these systems, as well as high quality renderings for visual exploration.

A collection of information about restriction enzymes and related proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequen ...

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.

EcoCyc is a model organism database for Escherichia coli K-12 MG1655. EcoCyc curation captures literature-based information on the functions of individual E. coli gene products, metabolic pathways, and regulation of E. coli gene expression. EcoCyc ha ...

CORUM is a database that provides a manually curated repository of experimentally characterized protein complexes from mammalian organisms, mainly human (64%), mouse (16%) and rat (12%). Each protein complex is described by a protein complex name, su ...

TDR Targets integrates chemical and genomic information and allows users to prioritize targets and compounds to develop and repurpose new drugs and chemical tools for human pathogens. The TDR Target Project was started in 2005 after a call for applic ...

MicroScope is a web-based platform for microbial comparative genome analysis and manual functional annotation. Its relational database schema stores precalculated results of syntactic and functional annotation pipelines as well as Pathway Tools and m ...

CottonGen is a cotton community genomics, genetics and breeding database being developed to enable basic, translational and applied research in cotton. It is being built using the open-source Tripal database infrastructure. CottonGen supercedes Cotto ...

FlyMine is an integrated database of genomic, expression and protein data for Drosophila, Anopheles and C. elegans. Its main focus is genomic and proteomics data for Drosophila and other insects. It provides access to integrated data at a number of d ...

DBETH is the Database of Bacterial Exotoxins for Human. The aim of this database is to assemble information on the toxins responsible for causing bacterial pathogenesis in humans.

TriTrypDB is one of the databases that can be accessed through the VEuPathDB portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these ...

Part of the Progenetix project, the arrayMap database facilitates the study of the genetics of human cancer. The Progenetix project provides the data customisation and visualization tools to mine the available data. The arrayMap database is developed ...

MaizeGDB is the maize research community's central repository for genetics and genomics information.

Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. Here we present the 3rd version of IMG/VR, composed of 18,373 cultivated and 2,314,329 uncultivated viral genomes (UViGs), n ...

The Swissregulon Database contains genome-wide annotations of regulatory sites. The predictions are based on Bayesian probabilistic analysis of a combination of input information including i) Experimentally determined binding sites reported in the li ...

SoyBase, the USDA-ARS soybean genetic database, is a comprehensive repository for professionally curated genetics, genomics and related data resources for soybean. SoyBase contains genetic, physical and genomic sequence maps integrated with qualitati ...

The euHCVdb is mainly oriented towards protein sequence, structure and function analyses and structural biology of Hepatitis C Virus.

The Arabidopsis Information Portal (Araport) is an open-access online community resource for Arabidopsis research. Araport enables biologists to navigate from the Arabidopsis thaliana Col-0 reference genome sequence to its associated annotation inclu ...

PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria.

Ensembl Bacteria is a browser for bacterial and archaeal genomes. These are taken from the databases of the International Nucleotide Sequence Database Collaboration (the European Nucleotide Archive at the EBI, GenBank at the NCBI, and the DNA Databas ...

For fast functional annotation of novel sequences. It uses precomputed orthologous groups and phylogenies from the eggNOG database to transfer functional information from fine-grained orthologs only. Its common uses include the annotation of novel ge ...

Genomics England PanelApp is a publicly-available knowledgebase that allows virtual gene panels related to human disorders to be created, stored and queried. It includes a crowdsourcing tool that allows genes and genomic entities (short tandem repeat ...

The Progenetix database provides an overview of copy number abnormalities in human cancer from Comparative Genomic Hybridization (CGH) experiments. With 30817 cases from 1016 publications (Oct 2013), Progenetix is the largest curated database for who ...

YEASTRACT (Yeast Search for Transcriptional Regulators And Consensus Tracking) is a curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 ...

PLEXdb (Plant Expression Database) is a unified gene expression resource for plants and plant pathogens. PLEXdb is a genotype to phenotype, hypothesis building information warehouse, leveraging highly parallel expression data with seamless portals to ...

The i5k Workspace@NAL has two main goals. First, it aims to help the i5k ‘data producers’, in particular ‘orphaned’ groups without the technical or financial means for genome hosting, at the interface of sequence retrieval and analysis. Specifically, ...

OrthoDB presents a catalog of eukaryotic orthologous protein-coding genes. Orthology refers to the last common ancestor of the species under consideration, and thus OrthoDB explicitly delineates orthologs at each radiation along the species phylogeny ...

GigaDB primarily serves as a repository to host data and tools associated with articles in GigaScience; however, it also includes a subset of datasets that are not associated with GigaScience articles. GigaDB defines a dataset as a group of files (e. ...

MycoCosm provides data access, visualization, and analysis tools for comparative genomics of fungi. MycoCosm enables users to navigate across sequenced fungal genomes, and to conduct comparative and genome-centric analyses of fungi and community anno ...

IMGT/GENE-DB is the IMGT® comprehensive genome database for immunoglobulins (IG) and T cell receptors (TR) genes from human and mouse, and, in developement, from other vertebrate species (e.g. rat). IMGT/GENE-DB is part of IMGT®, the international ...

The Aspergillus Genome Database is a resource for genomic sequence data as well as gene and protein information for Aspergilli. This publicly available repository is a central point of access to genome, transcriptome and polymorphism data for the fun ...

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of multi-omics data ...

The GenomeRNAi database collects RNAi phenotypes recorded in the literature for Homo sapiens and Drosophila melanogaster, as well as details on RNAi reagents. The data is well integrated with information from other resources, allowing comparison with ...

The Plant Ontology is a structured vocabulary and database resource that links plant anatomy, morphology and growth and development to plant genomics data. The PO is under active development to expand to encompass terms and annotations from all plant ...

The Ribosomal Database Project - II (RDP-II)(1) provides data, tools and services related to ribosomal RNA sequences to the research community. Through its website (http://rdp.cme.msu.edu), RDP-II offers aligned and annotated rRNA sequence data, anal ...

GnpIS is a multispecies integrative information system dedicated to plant and fungi pests. It bridges genetic and genomic data, allowing researchers access to both genetic information (e.g. genetic maps, quantitative trait loci, association genetics, ...

The Magnaporthe comparative genomics database provides accesses to multiple fungal genomes from the Magnaporthaceae family to facilitate the comparative analysis. The project is a partnership between the International Rice Blast Genome Consortium, an ...

The Animal Quantitative Trait Loci (QTL) Database (Animal QTLdb) strives to collect all publicly available trait mapping data, i.e. QTL (phenotype/expression, eQTL), candidate gene and association data (GWAS), and copy number variations (CNV) mapped ...

Influenza Virus Resource presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis, annotation and submission to GenBank. In addition, it provides links to other r ...

Access the data through the Ensembl user interface (both for visualisation and data mining) to provide cross-species integration throughout Ensembl's comparative genomics resources.

Analysis of finished and draft mouse genomic clone sequences.

Access to the Fly genome through the Ensembl user interface (both for visualisation and data mining).

This ensembl website features the zebrafish whole genome shotgun assembly sequence.

The Rat Genome project is an international collaboration to sequence the genome of the brown rat (Rattus norvegicus).

Fugu Ensembl is a joint project between The IMCB and the EMBL - EBI to produce and maintain an automatic annotation of the Fugu Genome.

The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology term ...

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 ...

NCBI Viral Genomes Resource is a collection of virus genomic sequences that provides curated sequence data, related information and tools. It includes all complete viral genome sequences deposited in the International Nucleotide Sequence Database Col ...

OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ort ...

UNITE is primarily a fungal rDNA internal transcribed spacer (ITS) sequence database, although they also welcome additional genes and genetic markers. UNITE focuses on high-quality ITS sequences generated from fruiting bodies collected and identified ...

Open TG-GATEs is a public toxicogenomics database developed so that a wider community of researchers could utilize the fruits of TGP and TGP2 research. This database provides public access to data on 170 of the compounds catalogued in TG-GATEs. Data ...

PhylomeDB is a public database for complete catalogs of gene phylogenies (phylomes). Researchers are able to use this resource to visualise the history of genes with the available phylogentic trees and multiple sequence alignments.

dictyBase is a single-access database for the complete genome sequence and expression data of four Dictyostelid species providing information on research, genome and annotations. There is also a repository of plasmids and strains held at the Dicty St ...

The Omics Discovery Index (OmicsDI) provides dataset discovery across a heterogeneous, distributed group of Transcriptomics, Genomics, Proteomics and Metabolomics data resources, including both open and controlled access data resources. The resource ...

ProtClustDB is a collection of related protein sequences (clusters) consisting of Reference Sequence proteins encoded by complete genomes. This database contains both curated and non-curated clusters.

REDfly is a curated collection of known Drosophila transcriptional cis-regulatory modules (CRMs) and transcription factor binding sites (TFBSs). REDfly seeks to include all experimentally verified fly regulatory elements along with their DNA sequence ...

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 ...

Gene expression and neuroanatomical data.

HAMAP is a system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies: the HAMAP families. HAMAP is based on manually created family rules and is appli ...

HumanMine integrates many types of data for Homo sapiens and Mus musculus. Users can run flexible queries, export results and analyse lists of data.

GeneDB is a genome database for prokaryotic and eukaryotic organisms and provides a portal through which data generated by the "Pathogen Genomics" group at the Wellcome Trust Sanger Institute and other collaborating sequencing centres can be accessed ...

Neuroimaging Informatics Tools and Resources Collaboratory Resources Registry (NITRC-R) describes software tools and resources, vocabularies, test data, and databases. It is intended to extend the impact and longevity of previously funded neuroimagin ...

This is a portal to the consensus yeast metabolic network as reconstructed from the genome sequence and literature. It is a highly annotated metabolic map of Saccharomyces cerevisiae S288c that is periodically updated by a team of collaborators from ...

Search and retrieve S. cerevisiae data with YeastMine, populated by SGD and powered by InterMine.

A detailed study of Giardia lamblia's genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.

INDIGO enables the integration of annotations for the exploration and analysis of newly sequenced microbial genomes.

The Human Genetic Variation Database (HGVD) aims to provide a central resource to archive and display Japanese genetic variation and association between the variation and transcription level of genes. The database currently contains genetic variation ...

BacDive—the Bacterial Diversity Metadatabase merges detailed strain-linked information on the different aspects of bacterial and archaeal biodiversity. BacDive contains entries for over 63,000 strains and provides information on their taxonomy, morph ...

FungiDB is an integrated genomic and functional genomic database for the kingdom Fungi. The database integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes compara ...

A suite of Web-based tools for comparative genomics

This database is compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects. The database makes it possible to continuously improve classification and characterization of retroviral families. The HERV database no ...

Gemma is a database for the meta-analysis, re-use and sharing of genomics data, currently primarily targeted at the analysis of gene expression profiles. Gemma contains data from thousands of public studies, referencing thousands of published papers. ...

A registry of Hereditary Auto-inflammatory Disorder Mutations.

The Hymenoptera Genome Database (HGD) is a genome informatics resource that supports the research of insects of the order Hymenoptera (e.g. bees, wasps, ants). HGD is divided into three main divisions: BeeBase, which hosts bee genomes and the Bee Pes ...

ThaleMine enables you to analyze Arabidopsis thaliana genes, proteins, gene expression, protein-protein interactions, orthologs, and more. Use plain text or structured queries for interactive gene and protein reports.

ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they mo ...

HumanCyc is a bioinformatics database that describes human metabolic pathways and the human genome. By presenting metabolic pathways as an organizing framework for the human genome, HumanCyc provides the user with an extended dimension for functional ...

Since 2016, the IMG/VR database has provided access to the largest collection of viral sequences obtained from (meta)genomes. The 3rd version of IMG/VR (Sept 2020) is composed of 18,373 cultivated and 2,314,329 uncultivated viral genomes (UViGs), nea ...

Aniseed is a database designed to offer a representation of ascidian embryonic development at the level of the genome (cis-regulatory sequences, spatial gene expression, protein annotation), of the cell (cell shapes, fate, lineage) or of the whole em ...

The DGVa team accepts direct submissions from researchers and also curates data from the published literature. As part of a regular exchange, DGVa data is sent to its partner archive, dbVar (hosted by the National Center for Biotechnology Information ...

Online Mendelian Inheritance in Animals is a a database of inherited disorders, other (single-locus) traits, and genes in animal species (other than human and mouse).

A web-based resource for integrative and conjugative elements (ICEs) found in bacteria. It collates available data from experimental and bioinformatics analyses, and literature, about known and putative ICEs in bacteria as a PostgreSQL-based database ...

The Golm Metabolome Database (GMD) provides gas chromatography (GC) mass spectrometry (MS) reference spectra, reference metabolite profiles and tools for one of the most widespread routine technologies applied to the large scale screening and discove ...

DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 197,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure I ...

The Banana Genome Hub centralises databases of genetic and genomic data for the Musa acuminata crop, and is the official portal for the Musa genome resources.

PlanMine is an integrated web resource of data & tools to mine Planarian biology.

dbSUPER is the first integrated and interactive database of super-enhancers, which contains 82234 super-enhancers in 102 human and 25 mouse tissue/cell types.

Sequence, structure and activity of protein toxins from spider venom

Corynebacterial Regulation Network a reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks.

The explosion in the number of functional genomic datasets generated with tools such as DNA microarrays has created a critical need for resources that facilitate the interpretation of large-scale biological data. SOURCE is a web-based database that b ...

HymenopteraMine integrates genomic data for bees, ants and the parasitoid jewel wasp. Expression and variation data are provided for A. mellifera.

Genome database of the beetle Tribolium castaneum

Collaborative resource for the Bacillus community.

The ApiDB website (http://eupathdb.org/eupathdb) represents a unified entry point for the NIH-funded Apicomplexan Bioinformatics Resource Center that integrates numerous database resources. The phylum Apicomplexa comprises numerous veterinary and med ...

MicrosporidiaDB is one of the databases that can be accessed through the EuPathDB (http://EuPathDB.org; formerly ApiDB) portal, covering eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Tricho ...

Type II Toxin-Antitoxin loci in bacteria and archaea

The Joint Genome Institute Genome Portal contains browseable and blastable genome assemblies for several organisms, including Pufferfish, Frog, and Sea squirt.

UK Biobank is a large-scale biomedical database and research resource that provides researchers access to detailed longitudinal phenotype, medical and genetic data from 500,000 volunteer participants.

The Human Ageing Genomic Resources (HAGR) is a collection of databases and tools for the biology and genetics of ageing. HAGR features several databases with high-quality, manually-curated data: 1) GenAge, a database of genes associated with ageing i ...

BovineMine integrates the bovine reference genome assembly with many other biological data sets, including genomes of other species. The sheep and goat genomes allow comparison across ruminants. Model organism data (human, mouse, rat) allow well-cura ...

The Prokaryotic Operon DataBase (ProOpDB) constitutes one of the most precise and complete repository of operon predictions in our days. Using our novel and highly accurate operon algorithm, we have predicted the operon structures of more than 1,200 ...

The Comprehensive Microbial Resource (CMR) gives access to a central repository of the sequence and annotation of all complete public prokaryotic genomes as well as comparative genomics tools across all of the genomes in the database.

BacMap is a picture atlas of annotated bacterial genomes. It is an interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.

The Aphid Genome Database's aim is to improve the current pea aphid genome assembly and annotation, and to provide new aphid genome sequences as well as tools for analysis of these genomes.

ProPortal is a database containing genomic, metagenomic, transcriptomic and field data for the marine cyanobacterium Prochlorococcus. They provide a source of cross-referenced data across multiple scales of biological organization—from the genome to ...

Mitochondrial genome database of fish with an accurate and automatic annotation pipeline.

ZebrafishMine is a tool to customize searches of Zebrafish-related biological data including genes, proteins, fish, and reagents

ViruSurf is a large public database of viral sequences and integrated and curated metadata from heterogeneous sources (RefSeq, GenBank, COG-UK and NMDC); it also exposes computed nucleotide and amino acid variants, called from original sequences. A G ...

TreeGenes is focused on connecting genomic, phenotypic, and environmental data for forest tree populations across the world. The database provides a custom informatics tools to manage the flood of information resulting from high-throughput genomics p ...

PDX Finder is an open repository for the upload and storage of clinical, genomic and functional Patient-Derived Xenograph (PDX) data which provides a comprehensive global catalogue of PDX models available for researchers across distributed repository ...

GreenPhylDB comprises 37 full genomes from the major phylum of plant evolution. Clustering of these genomes was performed to define a consistent and extensive set of homeomorphic plant families.

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

Dog Genome SNP Database (DoGSD) is a data container for the variation information of dog/wolf genomes. It was designed and constructed as an SNPs detector and visualization tool to provide the research community a useful resource for the study of dog ...

GermOnline is a cross-species database gateway focusing on high-throughput expression data relevant for germline development, the meiotic cell cycle and mitosis in healthy versus malignant cells. The portal provides access to the Saccharomyces Genomi ...

ALFRED is designed to make allele frequency data on human population samples readily available for use by the scientific and educational communities.

This project aims to support the international Aspergillus research community by gathering all genomic information regarding this significant genus into one resource - The Central Aspergillus REsource (CADRE). CADRE facilitates visualisation and anal ...

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.

FaceBase is a collaborative NIDCR-funded consortium to generate data in support of advancing research into craniofacial development and malformation. It serves as a community resource by generating large datasets of a variety of types and making them ...

Bacteriome.org is a database integrating physical (protein-protein) and functional interactions within the context of an E. coli knowledgebase.

GenoList is an integrated environment for comparative exploration of microbial genomes. The current release integrates genome data for over 700 species (Genome Reviews). The query and navigation user interface includes specialized tools for subtracti ...

NASA GeneLab expands scientists’ access to experiments that explore the molecular response of terrestrial biology to spaceflight environments. The vast amounts of raw data generated by experiments aboard the International Space Station are being made ...

ChlamDB is a comparative genomics database covering the entire Chlamydiae phylum as well as their closest relatives belonging to the Planctomycetes-Verrucomicrobiae-Chlamydiae (PVC) superphylum. Genomes can be compared, analyzed and retrieved using a ...

TreeBASE is a repository of phylogenetic information, specifically user-submitted phylogenetic trees and the data used to generate them. TreeBASE accepts all types of phylogenetic data (e.g., trees of species, trees of populations, trees of genes) re ...

Database which provides several ways to access to the grape genomic data: as a blast search page, a genome browser and a direct link to download the data.

The Oryzabase is a comprehensive rice science database established in 2000 by rice researcher's committee in Japan. The Oryzabase consists of five parts, (1) genetic resource stock information, (2) gene dictionary, (3) chromosome maps, (4) mutant ima ...

CHOmine integrates many types of data for Cricetulus griseus, and CHO cells. You can run flexible queries, export results and analyse lists of data.

To enable interoperability of genome annotations, we have developed the Genome Biology Ontology Language (GBOL) and associated stack (GBOL stack). GBOL is provenance centered and provides a consistent representation of genome derived automated predic ...

wFleaBase includes data from all species of the genus, yet the primary species are Daphnia pulex and Daphnia magna, because of the broad set of genomic tools that have already been developed for these animals.

DPVweb provides a central source of information about viruses, viroids and satellites of plants, fungi and protozoa. Comprehensive taxonomic information, including brief descriptions of each family and genus, and classified lists of virus sequences a ...

Predicted secreted bacterial proteins

ParameciumDB is a new model organism database for Paramecium, built using components of the Generic Model Organism Database (http://www.gmod.org) construction set (Chado relational database schema, Turnkey generic web framework and Gbrowse). The data ...

StellaBase is the Nematostella vectensis genomics database.

The MAR databases is a collection of manually curated marine microbial contextual and sequence databases, based at the Marine Metagenomics Portal. This was developed as a part of the ELIXIR EXCELERATE project in 2017 and is maintained by The Center f ...

Genomic data on mollicutes

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.

A web-based bacterial type IV secretion system resource for type IV secretion systems (T4SSs) and cognate effectors in bacteria.

Predicted proteins from C. elegans

Gene regulation in bacteriophages

An integrated Omics data warehouse for Locust, Locusta migratoria

The Mammalian Transcriptomic Database (MTD) was created to store information on mammalian transcriptomes. The MTD allows browsing of genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exo ...

SpodoBase is an integrated database for the genomics of the Lepidoptera Spodoptera frugiperda. It is a publicly available structured database with insect pest sequences which will allow identification of a number of genes and comprehensive cloning of ...

A CRISPR database for genome engineering.

FlyTF (v2) is a manually curated catalogue of Drosophila site-specific transcription factors (TFs). It integrates proteins identified as DNA-binding TFs by computational prediction based on structural domain assignments, and experimentally verified T ...

EchoBase is a database that curates new experimental and bioinformatic information about the genes and gene products of the model bacterium Escherichia coli K-12 strain MG1655.

The CFGP (Comparative Fungal Genomics Platform) was designed for comparative genomics projects with diverse fungal genomes.

A linked data server designed for ontologies. Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis. Ontobee dynamically dereferences and presents individual ontology term URIs to (i) HTML web pages for ...

Database of homologous genes from Ensembl organisms and Ensembl families, structured under ACNUC sequence database management system.

CyanoBase is the genome database for cyanobacteria, which are model organisms for photosynthesis. The database houses cyanobacteria species information, complete genome sequences, genome-scale experiment data, gene information, gene annotations and m ...

euGenes provides a common summary of gene and genomic information from eukaryotic organism databases including gene symbol and full name, chromosome, genetic and molecular map information, Gene Ontology (Function/Location/Process) and gene homology, ...

The UCSC Cancer Genomics Browser is a web-based tool to integrate, visualize and analyze cancer genomics and clinical data. The browser displays whole-genome views of experimental measurements for multiple samples, alongside their associated clinical ...

The Microbial Genome Database for Comparative Analysis (MBGD) is a database for comparative genomics based on comprehensive orthology analysis of bacteria, archaea and unicellular eukaryotes. MBGD now contains 6318 genomes. To utilize the database fo ...

The Ebola and Hemorrhagic Fever Virus Database stems from the Hemorrhagic Fever Viruses (HFV) Database Project founded by Dr. Carla Kuiken in 2009 at the Los Alamos National Laboratory (LANL). The HFV Database was modeled on the Los Alamos HIV Databa ...

Computational Bridge to Experiments

RNAiDB provides access to results from RNAi interference studies in C. elegans , including images, movies, phenotypes, and graphical maps.

This database provide several way to access to the genomic data, as a blast search page, a genome browser and a direct link to download the data.

The crop EST database CR-EST (http://pgrc.ipk-gatersleben.de/cr-est/) is a publicly available online resource providing access to sequence, classification, clustering, and annotation data of crop EST projects at IPK Gatersleben, Germany. CR-EST curre ...

Bacterial whole genome sequence typing database

IVDB hosts complete genome sequences of influenza A virus generated by BGI and curates all other published influenza virus sequences after expert annotations. IVDB provides a series of tools and viewers for analyzing the viral genomes, genes, genetic ...

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

Structural proteins of Arthropod cuticle

proGenomes is a database providing consistent taxonomic and functional annotations for 87,920 bacterial and archaeal genomes belonging to over 12,000 species. These can be interactively explored and downloaded, whereby subsets can be customized, e.g. ...

CIPRO is an integrated protein that has been developed to provide widespread information of the proteins expressed in the ascidian Ciona intestinalis, especially for the researcher who wants to get advance and useful information for starting biologic ...

An InterMine interface to data from Phytozome

RepetDB provides repeat consensus detected and classified by TEdenovo and used by TEannot to annotate copies in genomes.

Large-scale genomic data for the peanut have only become available in the last few years, with the advent of low-cost sequencing technologies. To make the data accessible to researchers and to integrate across diverse types of data, the International ...

XenMine has been created to view, search and analyze Xenopus data, and provides essential information on gene expression changes and regulatory elements present in the genome. It contains published genomic datasets from both Xenopus tropicalis and Xe ...

The D. melanogaster and eight other eukaryote model genomes, and gene predictions from several groups. Summaries of essential genome statistics include sizes, genes found and predicted, homology among genomes, phylogenetic trees of species, and compa ...

YPA (Yeast Promoter Atlas) is a repository of promoter features in Saccharomyces cerevisiae. It intergrates various resources (including promoter sequences, TSSs, TATA boxes, TFBSs, nucleosome occupancy, DNA bendability, TF-TF interaction, and gene e ...

Wiki for coordinating nematode sequencing projects

ODB (Operon DataBase) is a database of known operons among the many complete genomes. Additionally, putative operons that are conserved in terms of known operons are also provided. The first release of ODB conteins about 2000 known operons and 13,000 ...

SalmoBase is an integrated molecular resource for Salmonid species which includes visualizations and analytic tools. The genome of the Atlantic salmon (Salmo salar) has undergone extensive restructuring since a whole genome duplication event ~80 mill ...

Wiki database of biological databases

SilkDB is a database of the integrated genome resource for the silkworm, Bombyx mori. This database provides access to not only genomic data including functional annotation of genes, gene products and chromosomal mapping, but also extensive biologica ...

Gene Ontology-based functional similarity values for proteins and protein families

VIDA is a new virus database that organizes open reading frames from viral genomic sequences into virus-specific homologous protein families. Conserved sequence regions of potential functional importance are identified and can be retrieved as sequenc ...

InSatDb, unlike many other microsatellite databases that cater largely to the needs of microsatellites as markers, presents an interactive interface to query information regarding microsatellite characteristics of five fully sequenced insect genomes ...

EcoliWiki is a community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.

Brings together Docker images with standardized, machine-readable ways of describing and running the tools contained within.

Comparative genomics of Fusarium strains

Drosophila Polymorphism Database, is a secondary database designed to provide a collection of all the existing polymorphic sequences in the Drosophila genus. It allows, for the first time, the search for any polymorphic set according to different par ...

A database of eukaryotic sequencing projects

PanDrugs is a method to prioritize anticancer drug treatments according to individual genomic data. PanDrugs current version integrates data from 24 primary sources and supports 56297 drug-target associations obtained from 4804 genes and 9092 unique ...

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:.

Integrated database to study genomics, genetics and comparative genomics in Sesamum indicum.

The Total Integrated Archive of short-Read and Array (TIARA) accumulates raw-level personal genomic data from whole genome next-generation sequencing (NGS) and comparative genomic hybridization (CGH) arrays. Initially, it contains 36 individual genom ...

MarRef is a manually curated marine microbial genome database that contains complete genomes.

Includes all non-complete marine microbial genomes regardless of the level of completeness.

Public resource for genomic data extracted from species of Aspergillus. Array of online tools for searching and visualizing features are available.

Database and management system that provides an integrated set of bioinformatic tools to clone viral ORFs in the Gateway(R) system. It provides an interface to navigate through virus genome sequences, to design ORF-specific cloning primers, to valida ...

EK3D - an E. coli K antigen 3-dimensional structure database is a repository of 72 E. coli K antigens that provides information about the sugar composition, epimeric & enantiomeric forms and linkages between the sugar monomers.

Assembled partial genomes for ~250 eukaryotic organisms

Polymorphic Simple Sequence Repeats Database

IntOGen is a framework for automatic and comprehensive knowledge extraction based on mutational data from sequenced tumor samples from patients. The framework identifies cancer genes and pinpoints their putative mechanism of action across tumor types ...

a manually curated database of viral integration sites in the human genome. VISDB, visdb, virus integration site, viral integration, DNA virus, retrovirus, HBV, HPV, HIV, HTLV-1, EBV, AAV2, MCV, MLV, XMRV, gene, fragile site, miRNA, database, resour ...

A comprehensive database established to offer a web-based access to founder mutation data in Mediterranean population. The database provides an overview about the spectrum of founder mutations found in Mediterranean population to the scientific commu ...

The Tobacco Markers & Primers Database.

The eLibrary of Microbial Systematics and Genomics (eLMSG) database provides a platform for microbial systematics, genomics and phenomics (polyphasic taxonomy related phenotypes). It includes information in areas such as microbial taxonomy, ecology, ...

MedicMine integrates many types of data for Medicago truncatula. You can run flexible queries, export results and analyse lists of genes.

PeanutMine integrates peanut data from LIS PeanutBase and other sources.

This mine integrates many types of data for string bean built from the LIS chado database.

GrapeMine is dedicated to grapevine data. It provides access to many kind of data types like genomic annotation data as well as SNPs, markers and phenotyping data.

CowpeaMine integrates genomic and genetic data for cowpea, Vigna unguiculata. It is built from the LIS tripal.chado database as well as data from publications.

A genetic correlation is the proportion of shared variance between two traits that is due to genetic causes; a phenotypic correlation is the degree to which two traits co-vary among individuals in a population. In the genomics era, while gene express ...

This mine integrates many types of data for soybean. It is currently under development by LIS, built from the LIS chado database (genomic data) and the SoyBase database (genetic data) as well as other resources

WheatMine integrates many types of data for Triticum aestivum including gene model, markers, and scaffolds. You can run flexible queries, export results and analyse lists of data.

ChickpeaMine integrates data for chickpea varieties desi and kabuli. It is developed by LIS/NCGR, built from the LIS chado database and the Chickpea Transcriptome Atlas - I.

This mine integrates data for multiple legume species. It is under development by NCGR and is built from the LIS and PeanutBase chado databases as well as exports from other sources.

WormMine integrates many types of data for C. elegans and related nematodes. You can run flexible queries, export results and analyse lists of data.

The Ag Data Commons is a public, government, scientific research data catalog and repository available to help the agricultural research community share and discover research data funded by the United States Department of Agriculture and meet Federal ...

Domain-centric GO provides associations between ontological terms and protein domains at the superfamily and family levels. Some functional units consist of more than one domain acting together or acting at an interface between domains; therefore, on ...

RatMine integrates many types of data for Rattus Norvegicus, Homo Sapiens, Mus Musculus and other organisms. You can run flexible queries, export results and analyse lists of data.

The CSIRO Data Access Portal provides access to research data, software and other digital assets published by CSIRO across a range of disciplines. The portal is maintained by CSIRO Information Management & Technology to facilitate sharing and reuse.

The National Population Health Data Center (NPHDC) is one of the 20 national science data center approved by the Ministry of Science and Technology and the Ministry of Finance. The Population Health Data Archive (PHDA) is developed by NPHDC relying o ...

Repository of protein names and naming rules

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 ...

Phylogenetic Exploration of Viruses and their Evolutionary Relationships

The large-scale variant database of 1722 Koreans based on whole genome sequencing.

Making Omics Data Useful to the Broader Scientific Community. Metabolic Disorders Knowledge Portal. ||| CORRECT NAME OF TOOL COULD ALSO BE 'MSK-KP'

The GA4GH Toolkit outlines a suite of secure standards and frameworks that will enable more meaningful research and patient data harmonization and sharing. This suite addresses a variety of challenges across the data sharing life cycle and is applica ...

This is the place where you can find an updated list of the published mitochondrial sequences coming from the ancient DNA samples (aDNA). The main interest of our database lies in the anatomically modern Homo sapiens samples, ranging from the late Pa ...

GenoSurf is a metadata driven semantic search system for integrated genomic datasets. Many valuable resources developed by worldwide research institutions and consortia describe genomic datasets that are open, but their metadata search interfaces ar ...

A comprehensive catalogue of animal genome size data where haploid DNA contents (C-values, in picograms) are currently available for 4972 species (3231 vertebrates and 1741 non-vertebrates) based on 6518 records from 669 published sources.

The National Center for Research Resources' Yeast Resource Center is located at the University of Washington in Seattle, Washington. The mission of the center is to facilitate the identification and characterization of protein complexes in the yeast ...

A toolkit to cluster, evaluate, and extract non-redundant associations of Gene Ontology-based functions. GOMCL is a tool to cluster and extract summarized associations of Gene Ontology based functions in omics data. It clusters GO terms using MCL ba ...

Disease-Agnostic Gene Prioritization from High-Throughput Genomic Screens by Stochastic Semi-supervised Learning.

A database dedicated to long-range genome interactions quality assessment.

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

An Open-Access Platform for the Genomics of Brassica campestris (syn. Brassica rapa) ssp. chinensis.

A database of mitochondrial genome variants in chinese population

Model organism database for the bacterium Myxococcus xanthus.

The first integrated database of gene annotation and expression profiles for variants related to human diseases. An integrated database of variants and gene expression profiles for genetic diseases.

The Spirochetes Genome Browser

Data portal for the processing, analyzing, sharing and disseminating of metagenomic data sets

Genomics of fungal, oomycete and bacterial phytopathogens

Gene annotation portal and a resource on gene and protein function

The goal of the Genome Reviews project is to provide an up-to-date, standardised and comprehensively annotated view of the genomic sequence of organisms with completely deciphered genomes. Genome Reviews are curated versions of EMBL/GenBank/DDBJ dat ...

Whole-genome sequence data, variant calls, and annotations of natural genetic variation in C. elegans species.

The TBestDB (a Taxonomically Broad EST database) database contains ~370,000 clustered EST sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and includes experimental information, conse ...

Drosophila transgenic lines created using an intron protein trap strategy

Computational prediction of animal microRNA genes

Data resources at the European Bioinformatics Institute (EMBL-EBI, https://www.ebi.ac.uk/) archive, organize and provide added-value analysis of research data produced around the world. This year's update for EMBL-EBI focuses on data exchanges among ...

Interactions between HIV-1 and human proteins

Connecting genotype to phenotype is of fundamental importance in biomedical research and in our understanding of disease. Phenomics - large-scale analysis of gene function by quantitative analysis of phenotypes on a genome-wide scale - connects autom ...

Phenotypes of a large scale RNAi screen in the red flour beetle Tribolium castaneum

Fusarium graminearum Genome Database (FGDB) is a comprehensive genome database on one of the most devastating fungal plant pathogens of wheat and barley. FGDB provides information on two gene sets independently derived by automated annotation of the ...

The COGEME phytopathogen EST database currently contains expressed sequence tags (ESTs) from eleven species of phytopathogenic fungi and two oomycete species. In order to reduce sequence redundancy, sequence assembly software was used to join togethe ...

World Data Center of Microorganisms collections

GEISHA (Gallus Expression In Situ Hybridization Analysis) is a centralized and comprehensive repository of precise spatial and temporal information on chicken embryonic gene expression created through in situ hybridization. Annotations include probe ...

The UniProtKB Sequence/Annotation Version database (UniSave) is a comprehensive archive of UniProtKB/Swiss-Prot a nd UniProtKB/TrEMBL entry versions. All changed Swiss-Prot and TrEMBL entries are loaded into the UniSave as part of the public UniProtK ...

The HGTree database provides putative genome-wide horizontal gene transfer (HGT) information for 2,472 completely sequenced prokaryotic genomes. HGT detection is based on an explicit evolutionary model of tree reconstruction and relies on evaluating ...

The CONP portal is a web interface for the Canadian Open Neuroscience Platform (CONP) to facilitate open science in the neuroscience community. CONP simplifies global researcher access and sharing of datasets and tools. The portal internalizes the cy ...

Data views that bring together data from several LabKey tables for convenient access Quickviews bring together data from several LabKey tables for convenient access, including: rare_disease_analysis Data for all rare disease participants including: ...

This dataset brings together data from more than 500 local and regional datasets to build a picture of an individual’s treatment from diagnosis. Available for patients diagnosed with Cancer (ICD10 C00-97, D00-48) from 1 January 1995 -31 December 2017 ...

Cancer data are presented for either the patient level cancer diagnosis or “disease type” or the tumour specific sample details of participants in the Cancer arm of the 100,000 Genomes Project. Data Relating to Cancer Participants: cancer_participa ...

NHS national data sets collect information from care records, systems and organisations on specific areas of health and care. HES: Hospital Episode Statistics containing details of all commissioned activity during admissions, outpatient appointments ...

Contains tables with data related to genomic data and the outputs from the GEL interpretation pipeline data for participants from both cancer and rare disease programmes. These tables do not directly include primary + secondary sources of clinical da ...

Rare Disease (RD) data are presented at the level of RD families, RD pedigrees, and participants. Participants are consenting individuals who have had their genome sequenced. Pedigree members are extended members of the proband’s family. Rare Disease ...

Longitudinal, routine data for UHB NHSFT patients recruited to the 100K Genomes project that accessed Acute Care at UHB: This includes data for cancer and rare diseases in adults and children, with investigations undertaken and outcomes.

The UCLEB consortium of highly-phenotyped population-based prospective cohort studies provides a multi-omics data source consisting of genomics, metabolomics and proteomics for researching the molecular basis of disease and to inform drug development ...

COG-UK Consortium has published a dataset which contains over 20K SARS-CoV-2 viral genome sequences available as open access.

The INTERVAL bioresource comprises 50,000 English blood donors, on whom deep molecular phenotypes (e.g. genomics, proteomics, metabolomics, lipidomics) have been generated. In over 100 years of blood donation practice, INTERVAL is the first randomise ...

Complete Genomics provides free public access to a variety of whole human genome data sets generated from Complete Genomics’ sequencing service. The research community can explore and familiarize themselves with the quality of these data sets, review ...

>>>>!!!!<<<< The Cancer Genomics Hub mission is now completed. The Cancer Genomics Hub was established in August 2011 to provide a repository to The Cancer Genome Atlas, the childhood cancer initiative Therapeutically Applicable Research to Generate ...

Gene indices of human, mouse, zebrafish, Arabidopsis, and Drosophila

Conserved syntenies for various animal, plant and bacterial genomes

Complete Genome Tracking database

Genomic distribution of protein structural superfamilies

Community Cyberinfrastructure for Advanced Microbial Ecology Research and Analysis of metagenomic data

Sequences and classification of predicted membrane transporters encoded in complete genomes

EBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes

Genomics of two major lepidopteran pests.

NCBI's collection of databases for the analysis of complete and unfinished viral, pro- and eukaryotic genomes

Gowinda: unbiased analysis of gene set enrichment for Genome Wide Association Studies

Megx is a database portal for marine ecological genomics. This field of research is defined as: "the application of genomic sciences to understanding the structure and function of marine ecosystems". Megx.net includes:1) The "Genomes Mapserver": a ge ...

Databases of viral genomic information (genes, gene families, and genomes), and software to perform comparative genomics analyses

The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle gen ...

Genome annotation database of Drosophila

<<<!!!<<< Genome data generated by BC Genome Sciences Centre is no longer available through this site as it is regularly deposited into controlled data repositories such as the European Genome Phenome Archive (EGA); ICGC (International Cancer Genome ...

Intuitive and modular software platform designed to unify miRBase and independent miRNA data resources. It enables miRNA researchers to computationally address complex questions involving the multitude of miRNA data resources.

Nematode sequence and functional data database

Stanford Tuberculosis Database

The Microbial Genome Annotation Network (MGAN) is collaborating with the Genomics Education National Initiative (GENI), Dr. Cheryl Kerfeld (University of California - Berkley, CA) and Dr. Roy Welch (Syracuse University, NY) to provide authentic and i ...

Quercus robur annotation database

The Karyotype database (KaryotypeDB) contains karyotype and chromosome information like chromosome number, length, karyotype features, idiograms, physical localizations of DNA sequences by fluorescence in situ hybridizion (FISH), and cell material fo ...

Genomicus-fungi is a genome browser that enables users to navigate in fungi genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Network Extracted gene Ontology database

Insect genomes and transcriptomes

>>>!!<<<This is an archive of the old NEBC site from nebc.nerc.ac.uk and is no longer updated. For new information regarding NERC Environmental Omics and the Bio-Linux system please see the EOS site at http://environmentalomics.org. >>>!!!<<< ...

Genetic variation in Trypanosoma cruzi

Genomicus-protists is a genome browser that enables users to navigate in protists genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Trypanosoma cruzi genome database

yeast apoptosis database

Natural variation data in Caenorhabditis spp.

Genomicus-metazoa is a genome browser that enables users to navigate in metazoa genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

ESTs of the earthworm Lumbricus rubellus

Escherichia coli K-12 knowledgebase portal

The Actinobacteriophage Database.

A knowledge database for the Hepatitis B Virus

Human Pan-Microbial Communities Database

Transcription regulation in pathogenic yeasts

Database of the Drosophila nervous system

SYSTOMONAS (SYSTems biology of pseudOMONAS, http://www.systomonas.de) is a database on pseudomonads providing data and tools on metabolic network reconstruction, gene-regulatory networks, visualization of genomic structures or metabolic pathways, com ...

SNP data for Drosophila melanogaster

The Schmidtea mediterranea genome database

Gene Ontology Normal Usage Tracking System

Human Cell Lines Identification Resources

Microbial knowledge exploration systems

List of Prokaryotic names with Standing in Nomenclature

Database of alternate open reading frames

FlyAtlas: the Drosophila gene expression atlas

Aeschynomene evenia genomic data from the Legume Information System

The Cancer Cell Line Encyclopedia project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacolog ...

This genomic tRNA database contains tRNA identifications made by the program tRNAscan-SE (Lowe & Eddy, Nucl Acids Res 25: 955-964, 1997) on complete or nearly complete genomes. Unless otherwise noted, all annotation is automated, and has not been ins ...

antibiotics and Secondary Metabolite Analysis SHell

Genomicus-tunicates is a genome browser that enables users to navigate in tunicates genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time. It uses ANISEED (htt ...

Prokaryotic virus orthologous groups of proteins

microRNAs targets of the influenza virus

Integrative database around plant genomes.

Disease and Gene Annotations database

E. coli genome database at Institut Pasteur

Biochemical pathways of Trypanosoma brucei

Metagenomic catalog of clade-specific microbial genes

A database for E. coli, Salmonella and Shigella

Genome of the pea aphid symbiont Buchnera sp. APS

An integrated Omics data warehouse for FAW, Spodoptera frugiperda

A database on the nematode Pristionchus pacificus

A database of Papillomaviridae family of viruses

Sex bias in insect gene expression database

Similarity-based classification of chemical compounds

Genome analysis of Plasmodium, Entamoeba, Trypanosoma and Leishmania

Regulatory pathways during the sporulation cycle of Bacillus subtilis

Information on phylogeny and biodiversity

The South Green Genome Hub is a suite of crop-specific community portals to manage genomic datasets with focus on tropical and Mediterranean plants. Currently developed on Banana, Cassava, Cacao, Coffee, Grass, Rice and Sugarcane, genome hubs provide ...

Localization and Quantitation Atlas of the Yeast Proteome

An integrated data warehouse for MaizeGDB

White and narrow-leaf lupin data from the Legume Information System

Drosophila genes and their roles in development

>>>!!!<<< Noticed 26.08.2020: The NCI CBIIT instance of the CGAP no longer exist on this website. The Mitelman Database of Chromosome Aberrations and Gene Fusions in Cancer has a new home at the NCI-funded Institute for Systems Biology Cancer Geno ...

A database for multilocus sequence typing analysis of the Bacillus cereus group of bacteria

A reference collection of viral ORFs and their clones

Escherichia coli K-12 in-frame, single-gene knockout mutants

3'UTRs and their functional elements in C. elegans

Cryptosporidium parvum genome database

Cell cycle program of Caulobacter crescentus

Metabolic evolution resource and its application to Plasmodium evolution

The Pathosystems Resource Integration Center (PATRIC) is the all-bacterial Bioinformatics Resource Center (BRC) (http://www.patricbrc.org). A joint effort by two of the original NIAID-funded BRCs[1,2], PATRIC provides researchers with an online resou ...

Database for comparative genome analysis of 15 strains of the genus Streptococcus

Parasitic nematode sequencing project

Chemogenomic experiments in yeast: connection of drug response to biological pathways, phenotypes, and networks

Integr8 is a new web portal for exploring the biology of organisms with completely deciphered genomes. For over 190 species, Integr8 provides access to general information, recent publications, and a detailed statistical overview of the genome and pr ...

Computational models for gene silencing in C. elegans

PCR primer pairs for detecting RNA virus-mediated infectious diseases

Database and knowledgebase of authenticated microbial genomics data with full data provenance to physical materials held within American Type Culture Collection's (ATCC) biorepository and culture collections. Data includes whole genome sequencing dat ...

Developmental phenomics, cell-specific gene functions and cell differentiation in C. elegans

Microarray datasets for microbial gene expression

Genomicus-Plants is a genome browser that enables users to navigate in plants genomes in several dimensions: linearly along chromosome axes, transversaly across different species, and chronologicaly along evolutionary time.

Unified Aspergillus resource with medical and genomic data

In light of the rapid decrease in fossils fuel reserves and an increasing demand for energy, novel methods are required to explore alternative biofuel production processes to alleviate these pressures. A wide variety of molecules which can either be ...

Poxvirus genomic sequences and gene annotation

The Open Archive for Miscellaneous Data (OMIX) database is a data repository developed and maintained by the National Genomics Data Center (NGDC). The database specializes in descriptions of biological studies, including genomic, proteomic, and metab ...

Ashbya gossypii genome database

Yeast small nucleolar RNAs

Database of genomic data related to marine species of biological interest. It allows analyses of reference genome annotations, organising the resources in an integrated way

Pairwise-comparisons Of Genomes and universal Orthologous genes

First results of an E. coli gene deletion project

The Host-Pathogen Interaction Database of Pseudomonas aeruginosa and Coxiella spp.

E. coli database at U. Alberta

Predicted highly expressed genes in prokaryotic genomes

An integrated omics database for functional genomic analysis of cyanobacteria.

A suite of Web-based comparative genomic tools for metagenome analysis

INVHOGEN (INVertebrate HOmologous GENes) is a database combining the available invertebrate protein genes from UniProt (consisting of Swiss-Prot, TrEMBL) into gene families. For each family INVHOGEN provides a multiple protein alignment, a maximum li ...

Atlas of Biosynthetic gene Clusters for secondary metabolites

An integrative database of cancer-associated viruses.

Genome database of microbial photosynthetic eukaryotes.

Database of essential genes from bacteria and yeast

Community analysis of E. coli and related genomes

A comprehensive enrichment analysis software for human genomic regions.

A data-driven social network connecting scientists to genomics datasets. ORSO (Online Resource for Social Omics) is a web application designed to help users find next generation sequencing (NGS) datasets relevant to their research interests. ORSO per ...

Complete genomic profiles of 1,496 Taiwanese reveal curated medical insights.

A database of yeast promoters

ESTs from two diatom algae, Thalassiosira pseudonana and Phaeodactylum tricornutum

Comprehensive database on E. coli genome

Yeast expression data

Platform for storing and using pangenomes for imputation.

Database of Cork Oak EST sequences from the Portuguese Cork Oak sequencing project.

A comprehensive database of nucleosome organization referenced landscapes in mammalian genomes.

The PEDANT genome database (http://pedant.gsf.de) provides exhaustive automatic analysis of genomic sequences by a large variety of established bioinformatics tools through a comprehensive Web-based user interface. Nearly 3000 completely sequenced pu ...

A genome database for the genus Piroplasma. PiroplasmaDB is a member of pathogen-databases that are housed under the NIAID-funded EuPathDB Bioinformatics Resource Center (BRC) umbrella.

Bacillus subtilis genome database at Kyoto U.

smiRNAdb is a database containing expression information for human, mouse, rat, zebrafish, worm and fruitfly small RNAs (mostly miRNAs).

DupScan is a database for visualizing and predicting vertebrate synteny and genome duplication.

A disorders of sex development atlas for reproductive endocrinology-related gene discovery in integrative omics platforms.

Comprehensive drug discovery and genomic research workbench, knowledgebase and data management system.

Community database centralizing genomic and transcriptomic sequence information for ants and related species (e.g., bees and wasps). Provides BLAST search and data download. Updated periodically with latest data and new tools.

NetPath is currently one of the largest open-source repository of human signaling pathways that is all set to become a community standard to meet the challenges in functional genomics and systems biology. Signaling networks are the key to deciphering ...

Influenza is one of the most important respiratory infectious diseases of humans. It is estimated that influenza is responsible for 250,000 to 500,000 deaths annually. Genome sequences of currently circulating virus isolates are important sources of ...

Yeast deletion project and mitochondria database

Rhododendron Plant Genome Database (RPGD) is a comprehensive online omics database for Rhododendron.

The NCBI Nucleotide database collects sequences from such sources as GenBank, RefSeq, TPA, and PDB. Sequences collected relate to genome, gene, and transcript sequence data, and provide a foundation for research related to the biomedical field.

ShiBASE (http://www.mgc.ac.cn/ShiBASE/) is a freely accessible online resource that is focused on the comparative genomics of Shigella. ShiBASE is able to summarize large volumes of genomic sequence and comparative genomic data in a visually intuitiv ...

MVIP provides a large number of available multi-omics data under viral infection in various species.

Branch of BioModels Database dedicated to hosting models automatically generated from pathway resources, such as KEGG, BioCarta, MetaCyc, PID and SABIO-RK.

The MIRIAM Registry provides a set of services for the generation of unique and perennial identifiers, in the form of URIs. The core of the Registry is a catalogue of data collections (corresponding to controlled vocabularies, databases, etc.)

A simple access point to view gene family assignments, annotations and phylogenetic data for insect immune-related genes and gene families.

Multi-ethnic database for identifying copy number variations associated with cancer. View gene-centric CNV profile collected from healthy individuals and multiple cancer types.

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, ...

The Sugarcane Genome Hub is an integrated web-based database providing centralized access to the sugarcane reference genome sequences and genomic resources.

A database of paralogs and single copy genes in Arabidopsis thaliana. Database of single copy and duplicated genes in the Arabidopsis genome. It is a collection that integrates comparative results at genomic level to identify any form of gene duplica ...

LeptoList is the reference database dedicated to the genome of Leptospira interrogans serovar Lai, the paradigm of leptospirosis causative agents (1). It has been developed as a spin-off of the B. subtilis genome project (2), GenoList provides a data ...

CBS offers Comprehensive public databases of DNA- and protein sequences, macromolecular structure, g ene and protein expression levels, pathway organization and cell signalling, have been established to optimise scientific exploitation of the explosi ...

Clinical Genomic Database (CGD) is a manually curated database of conditions with known genetic causes, focusing on medically significant genetic data with available interventions.

The OpenFlu database (OpenFluDB) is part of a collaborative effort to share observations on the evolution of Influenza virus in both animals and humans. It contains genomic and protein sequences as well as epidemiological data from more than 25'000 i ...

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This is a animal and human genome database that uses the BioMart software.

PathCards is an integrated database of human biological pathways and their annotations. Human pathways were clustered into SuperPaths based on gene content similarity. Each PathCard provides information on one SuperPath which represents one or more h ...

Database of fungal genome size information has been launched in 2005: the Fungal Genome Size Database (http://www.zbi.ee/fungal-genomesize/). The database provides freely accessible genome size data assembled from literature. The taxonomy and the nam ...

Long-read-tools is an interactive database of software tools for the analysis of long read sequencing data.

The NCBI Entrez Genome Project database is intended to be a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. The database is organized into organ ...

proMGE is a resource for the retrieval of 6 Mobile Genetic Element (MGE) categories in 76K genomes (totalling to 2.4 million prokaryotic MGEs) and classification of new ones in user provided protein sequences from genomes and genomic fragments.

Integrated large scale dataset facilitating Big Data analysis in chemogenomics.

Genome track alignments using GBrowse on this site are featured with: (1) Annotated and predicted genes and transcripts; (2) QTL / SNP Association tracks; (3) OMIA genes; (4) Various SNP Chip tracks; (5) Other mapping fetures or elements that are ava ...

MtbRegList is a database dedicated to the analysis of gene expression and regulation data in Mycobacterium tuberculosis. It is designed to contain predicted and characterized regulatory DNA motifs cross-referenced with corresponding transcription fac ...