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Found 253 result(s)
The Bacterial and Viral Bioinformatics Resource Center (BV-BRC) is an information system designed to support research on bacterial and viral infectious diseases. BV-BRC combines two long-running BRCs: PATRIC, the bacterial system, and IRD/ViPR, the viral systems.
The Wellcome Trust Sanger Institute is a charitably funded genomic research centre located in Hinxton, nine miles south of Cambridge in the UK. We study diseases that have an impact on health globally by investigating genomes. Building on our past achievements and based on priorities that exploit the unique expertise of our Faculty of researchers, we will lead global efforts to understand the biology of genomes. We are convinced of the importance of making this research available and accessible for all audiences. reduce global health burdens.
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Oral Cancer Gene Database is an initiative of the Advanced Centre for Treatment, Research and Education in Cancer, Navi Mumbai. The present database, version II, consists of 374 genes. It is developed as a user friendly site that would provide the scientist, information and external links from one place. The database is accessed through a list of all genes, and Keyword Search using gene name or gene symbol, chromosomal location, CGH (in %), and molecular weight. Interaction Network shows the interaction between genes for particular biological processes and molecular functions.
TriTrypDB is an integrated genomic and functional genomic database for pathogens of the family Trypanosomatidae, including organisms in both Leishmania and Trypanosoma genera. TriTrypDB and its continued development are possible through the collaborative efforts between EuPathDB, GeneDB and colleagues at the Seattle Biomedical Research Institute (SBRI).
BiGG is a knowledgebase of Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions. BiGG integrates several published genome-scale metabolic networks into one resource with standard nomenclature which allows components to be compared across different organisms. BiGG can be used to browse model content, visualize metabolic pathway maps, and export SBML files of the models for further analysis by external software packages. Users may follow links from BiGG to several external databases to obtain additional information on genes, proteins, reactions, metabolites and citations of interest.
Giardia lamblia is a significant, environmentally transmitted, human pathogen and an amitochondriate protist. It is a major contributor to the enormous worldwide burden of human diarrheal diseases, yet the basic biology of this parasite is not well understood. No virulence factor has been identified. The Giardia lamblia genome contains only 12 million base pairs distributed onto five chromosomes. Its analysis promises to provide insights about the origins of nuclear genome organization, the metabolic pathways used by parasitic protists, and the cellular biology of host interaction and avoidance of host immune systems. Since the divergence of Giardia lamblia lies close to the transition between eukaryotes and prokaryotes in universal ribosomal RNA phylogenies, it is a valuable, if not unique, model for gaining basic insights into genetic innovations that led to formation of eukaryotic cells. In evolutionary terms, the divergence of this organism is at least twice as ancient as the common ancestor for yeast and man. A detailed study of its genome will provide insights into an early evolutionary stage of eukaryotic chromosome organization as well as other aspects of the prokaryotic / eukaryotic divergence.
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Edmond is the institutional repository of the Max Planck Society for public research data. It enables Max Planck scientists to create citable scientific assets by describing, enriching, sharing, exposing, linking, publishing and archiving research data of all kinds. Further on, all objects within Edmond have a unique identifier and therefore can be clearly referenced in publications or reused in other contexts.
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.
Candida Genome Database, a resource for genomic sequence data and gene and protein information for Candida albicans and related species. CGD is based on the Saccharomyces Genome Database. The Candida Genome Database (CGD) provides online access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans and related species. C. albicans is the best studied of the human fungal pathogens. It is a common commensal organism of healthy individuals, but can cause debilitating mucosal infections and life-threatening systemic infections, especially in immunocompromised patients. C. albicans also serves as a model organism for the study of other fungal pathogens.
RADAR service offers the ability to search for research data descriptions of the Natural Resources Institute Finland (Luke). The service includes descriptions of research data for agriculture, forestry and food sectors, game management, fisheries and environment. The public web service aims to facilitate discovering subjects of natural resources studies. In addition to Luke's research data descriptions one can search metadata of the Finnish Environment Institute (SYKE). The interface between Luke and SYKE metadata services combines Luke's research data descriptions and SYKE's descriptions of spatial datasets and data systems into a unified search service.
VectorBase provides data on arthropod vectors of human pathogens. Sequence data, gene expression data, images, population data, and insecticide resistance data for arthropod vectors are available for download. VectorBase also offers genome browser, gene expression and microarray repository, and BLAST searches for all VectorBase genomes. VectorBase Genomes include Aedes aegypti, Anopheles gambiae, Culex quinquefasciatus, Ixodes scapularis, Pediculus humanus, Rhodnius prolixus. VectorBase is one the Bioinformatics Resource Centers (BRC) projects which is funded by National Institute of Allergy and Infectious Diseases (NAID).
enviPath is a database and prediction system for the microbial biotransformation of organic environmental contaminants. The database provides the possibility to store and view experimentally observed biotransformation pathways. The pathway prediction system provides different relative reasoning models to predict likely biotransformation pathways and products.
dictyBase is an integrated genetic and literature database that contains published Dictyostelium discoideum literature, genes, expressed sequence tags (ESTs), as well as the chromosomal and mitochondrial genome sequences. Direct access to the genome browser, a Blast search tool, the Dictyostelium Stock Center, research tools, colleague databases, and much much more are just a mouse click away. Dictybase is a genome portal for the Amoebozoa. dictyBase is funded by a grant from the National Institute for General Medical Sciences.
The database aims to bridge the gap between agent repositories and studies documenting the effect of antimicrobial combination therapies. Most notably, our primary aim is to compile data on the combination of antimicrobial agents, namely natural products such as AMP. To meet this purpose, we have developed a data curation workflow that combines text mining, manual expert curation and graph analysis and supports the reconstruction of AMP-Drug combinations.
The MG-RAST server is an open source system for annotation and comparative analysis of metagenomes. Users can upload raw sequence data in fasta format; the sequences will be normalized and processed and summaries automatically generated. The server provides several methods to access the different data types, including phylogenetic and metabolic reconstructions, and the ability to compare the metabolism and annotations of one or more metagenomes and genomes. In addition, the server offers a comprehensive search capability. Access to the data is password protected, and all data generated by the automated pipeline is available for download in a variety of common formats. MG-RAST has become an unofficial repository for metagenomic data, providing a means to make your data public so that it is available for download and viewing of the analysis without registration, as well as a static link that you can use in publications. It also requires that you include experimental metadata about your sample when it is made public to increase the usefulness to the community.
<<<!!!<<< 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.
<<<!!!<<< 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.
The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids. These are the molecules of life that are found in all organisms including bacteria, yeast, plants, flies, other animals, and humans. Understanding the shape of a molecule helps to understand how it works. This knowledge can be used to help deduce a structure's role in human health and disease, and in drug development. The structures in the archive range from tiny proteins and bits of DNA to complex molecular machines like the ribosome.
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<<<!!!<<< 2017-06-02: We recently suffered a server failure and are working to bring the full ORegAnno website back online. In the meantime, you may download the complete database here: http://www.oreganno.org/dump/ ; Data are also available through UCSC Genome Browser (e.g., hg38 -> Regulation -> ORegAnno) https://genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=686342163_2it3aVMQVoXWn0wuCjkNOVX39wxy&c=chr1&g=oreganno >>>!!!>>> The Open REGulatory ANNOtation database (ORegAnno) is an open database for the curation of known regulatory elements from scientific literature. Annotation is collected from users worldwide for various biological assays and is automatically cross-referenced against PubMED, Entrez Gene, EnsEMBL, dbSNP, the eVOC: Cell type ontology, and the Taxonomy database, where appropriate, with information regarding the original experimentation performed (evidence). ORegAnno further provides an open validation process for all regulatory annotation in the public domain. Assigned validators receive notification of new records in the database and are able to cross-reference the citation to ensure record integrity. Validators have the ability to modify any record (deprecating the old record and creating a new one) if an error is found. Further, any contributor to the database can comment on any annotation by marking errors, or adding special reports into function as they see fit. These features of ORegAnno ensure that the collection is of the highest quality and uniquely provides a dynamic view of our changing understanding of gene regulation in the various genomes.
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The GISAID Initiative promotes the international sharing of all influenza virus sequences, related clinical and epidemiological data associated with human viruses, and geographical as well as species-specific data associated with avian and other animal viruses, to help researchers understand how the viruses evolve, spread and potentially become pandemics. *** GISAID does so by overcoming disincentives/hurdles or restrictions, which discourage or prevented sharing of influenza data prior to formal publication. *** The Initiative ensures that open access to data in GISAID is provided free-of-charge and to everyone, provided individuals identify themselves and agree to uphold the GISAID sharing mechanism governed through its Database Access Agreement. GISAID calls on all users to agree to the basic premise of upholding scientific etiquette, by acknowledging the originating laboratories providing the specimen and the submitting laboratories who generate the sequence data, ensuring fair exploitation of results derived from the data, and that all users agree that no restrictions shall be attached to data submitted to GISAID, to promote collaboration among researchers on the basis of open sharing of data and respect for all rights and interests.
The UniPROBE (Universal PBM Resource for Oligonucleotide Binding Evaluation) database hosts data generated by universal protein binding microarray (PBM) technology on the in vitro DNA binding specificities of proteins. This initial release of the UniPROBE database provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ('words') of length k ('k-mers'), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. In total, the database currently hosts DNA binding data for 406 nonredundant proteins from a diverse collection of organisms, including the prokaryote Vibrio harveyi, the eukaryotic malarial parasite Plasmodium falciparum, the parasitic Apicomplexan Cryptosporidium parvum, the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, mouse, and human. The database's web tools (on the right) include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences