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Found 131 result(s)
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's population, evolution, phenotype and life habit.
Clinical Genomic Database (CGD) is a manually curated database of conditions with known genetic causes, focusing on medically significant genetic data with available interventions.
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 biological information such as microarray expression data, ESTs and corresponding references. SilkDB will be useful for the silkworm research community as well as comparative genomics
This Web resource provides data and information relevant to SARS coronavirus. It includes links to the most recent sequence data and publications, to other SARS related resources, and a pre-computed alignment of genome sequences from various isolates. The genome of SARS-CoV consists of a single, positive-strand RNA that is approximately 29,700 nucleotides long. The overall genome organization of SARS-CoV is similar to that of other coronaviruses. The reference genome includes 13 genes, which encode at least 14 proteins. Two large overlapping reading frames (ORFs) encompass 71% of the genome. The remainder has 12 potential ORFs, including genes for structural proteins S (spike), E (small envelope), M (membrane), and N (nucleocapsid). Other potential ORFs code for unique putative SARS-CoV-specific polypeptides that lack obvious sequence similarity to known proteins.
MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features.
ALFRED is a free, web-accessible, curated compilation of allele frequency data on DNA sequence polymorphisms in anthropologically defined human populations. ALFRED is distinct from such databases as dbSNP, which catalogs sequence variation.
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 ortholog groups in Bacteria and Archaea. The Ortholuge method improves the specificity of high-throughput orthology prediction.
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. Users can search, access and visualize co-expression and differential expression results.
Content type(s)
BioSamples stores and supplies descriptions and metadata about biological samples used in research and development by academia and industry. Samples are either 'reference' samples (e.g. from 1000 Genomes, HipSci, FAANG) or have been used in an assay database such as the European Nucleotide Archive (ENA) or ArrayExpress.
ArrayExpress is one of the major international repositories for high-throughput functional genomics data from both microarray and high-throughput sequencing studies, many of which are supported by peer-reviewed publications. Data sets are either submitted directly to ArrayExpress and curated by a team of specialist biological curators, or are imported systematically from the NCBI Gene Expression Omnibus database on a weekly basis. Data is collected to MIAME and MINSEQE standards.
ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data collected by or in collaboration with researchers at the University of Wisconsin - Madison. ASAP was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, and gene expression data from preliminary experiments.
>>>>!!!!<<<< 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 Effective Treatments and the Cancer Genome Characterization Initiative. CGHub rapidly grew to be the largest database of cancer genomes in the world, storing more than 2.5 petabytes of data and serving downloads of nearly 3 petabytes per month. As the central repository for the foundational genome files, CGHub streamlined team science efforts as data became as easy to obtain as downloading from a hard drive. The convenient access to Big Data, and the collaborations that CGHub made possible, are now essential to cancer research. That work continues at the NCI's Genomic Data Commons. All files previously stored at CGHub can be found there. The Website for the Genomic Data Commons is here: >>>>!!!!<<<< The Cancer Genomics Hub (CGHub) is a secure repository for storing, cataloging, and accessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects. Access to CGHub Data: All researchers using CGHub must meet the access and use criteria established by the National Institutes of Health (NIH) to ensure the privacy, security, and integrity of participant data. CGHub also hosts some publicly available data, in particular data from the Cancer Cell Line Encyclopedia. All metadata is publicly available and the catalog of metadata and associated BAMs can be explored using the CGHub Data Browser.
This site provides access to complete, annotated genomes from bacteria and archaea (present in the European Nucleotide Archive) through the Ensembl graphical user interface (genome browser). Ensembl Bacteria contains genomes from annotated INSDC records that are loaded into Ensembl multi-species databases, using the INSDC annotation import pipeline.
SoyBase is a professionally curated repository for genetics, genomics and related data resources for soybean. It contains current genetic, physical and genomic sequence maps integrated with qualitative and quantitative traits. SoyBase includes annotated "Williams 82" genomic sequence and associated data mining tools. The repository maintains controlled vocabularies for soybean growth, development, and traits that are linked to more general plant ontologies.
The Crop EST Database (CR-EST) is a public available online resource providing access to sequence, classification, clustering, and annotation data of crop EST projects at the IPK. A view of these information give the summarized numbers about genomic data of species listed in the adjacent table.
BioMagResBank (BMRB) is the publicly-accessible depository for NMR results from peptides, proteins, and nucleic acids recognized by the International Society of Magnetic Resonance and by the IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. In addition, BMRB provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR
DDBJ; DNA Data Bank of Japan is the sole nucleotide sequence data bank in Asia, which is officially certified to collect nucleotide sequences from researchers and to issue the internationally recognized accession number to data submitters.Since we exchange the collected data with EMBL-Bank/EBI; European Bioinformatics Institute and GenBank/NCBI; National Center for Biotechnology Information on a daily basis, the three data banks share virtually the same data at any given time. The virtually unified database is called "INSD; International Nucleotide Sequence Database DDBJ collects sequence data mainly from Japanese researchers, but of course accepts data and issue the accession number to researchers in any other countries.
The dbVar is a database of genomic structural variation containing data from multiple gene studies. Users can browse data containing the number of variant cells from each study, and filter studies by organism, study type, method and genomic variant. Organisms include human, mouse, cattle and several additional animals. ***NCBI will phase out support for non-human organism data in dbSNP and dbVar beginning on September 1, 2017 ***
Content type(s)
A small genotype data repository containing data used in recent papers from the Estonian Biocentre. Most of the data pertains to human population genetics. PDF files of the papers are also freely available.
CORUM is a manually curated dataset of mammalian protein complexes. Annotation of protein complexes includes protein complex composition and other valuable information such as method of purification, cellular function of complexes or involvement in diseases.
The Taenia solium genome project is a whole genome sequencing project of the parasite Taenia solium, the causal agent of human and porcine cysticercosis; a disease that is still a public health problem of relevance in Mexico. It is being carried out by a consortium of scientists belonging to diverse institutions of the Universidad Nacional Autónoma de México (UNAM, the National Autonomous University of Mexico).
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 available.
>>>!!!<<< 08.08.2019: Plexdb is no longer online, URLold: >>>!!!<<< >>>>!!!! <<<< 13.12.2018: PLEXdb is now a static site after funding stopped from NSF. We have stopped registration of new users; but past users who have data can login when needed and interact with the site. You can download data using the authentication provided at the download page. >>>>!!!!<<<< PLEXdb 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 related genetic, physical, and pathway data.