Services: Data Resources

A data resource for Quercus suber.

Czech COVID-19 genomics portal

CRISPRCas++ is a new website holding a program called CRISPRCasFinder to detect CRISPR arrays and cas genes in the genome of prokaryotes. CRISPRCasMeta is adapted to the analysis of large metagenomic data. The programs are available online or can be downloaded for local usage. A database called CRISPRCasdb, the successor of CRISPRdb, is accessible on the CRISPRCas++ website. It can be browsed and queried in search for repeat and spacer sequences. 

Research data management platform to enable researchers to produce FAIR data by design  

The German epigenome programme ‘DEEP’ is an interdisciplinary research network. Its goal is to generate data for biomedical interpretation of healthy and diseased cells. With this, DEEP will contribute to discover new functional epigenetic links useful for clinical diagnosis, therapy and health risk prevention. 

Database of human genes with their probability of being involved in a
hereditary disease (emerging service) 

Aan interactive, web-based exploratory data analytics application providing access to over 1,000 Dictyostelium gene expression experiments from Baylor College of Medicine.

We provide support and guidance in development of Disease Maps (disease-maps.org), computational and visual repositories of knowledge about mechanisms of human diseases. We offer hosting of open access Disease Maps on the MINERVA Platform (minerva-web.lcsb.uni.lu) on our infrastructure under the elixir-luxembourg.org sub-domain, their backup and conservation. The MINERVA Platform ensures online access, interactive exploration, search for known drug targets and visualisation of omics datasets. We provide training in management of the Disease Maps and guidance to their integration into reproducible computational workflows by using the dedicated API of the hosting platform.

A manually curated community resource annotating proteins for experimentally determined regions of intrinsic disorder from the literature.

Database Of Local Biomolecumal COnfromers. (Formerly known as DOLCE)

This resource includes sequence pipeline (TarO) analysis, a secondary prediction (JPred) structure server, and a protein kinase database and kinase classification pipeline (Kinomer).

EMPIAR, the Electron Microscopy Public Image Archive, is a public resource for raw, 2D electron microscopy images: it allows users to upload, and download and reprocess the thousands of raw, 2D images used to build a 3D structure.

The Electron Microscopy Data Bank (EMDB) is a public repository for electron microscopy density maps of macromolecular complexes and subcellular structures. It covers a variety of techniques, including single-particle analysis, electron tomography, and electron (2D) crystallography.

Produces and maintains automatic and manually curated annotation on eukaryotic genomes. It is integrated with important molecular resources, for example UniProt, and can be accessed programmatically or through a web browser.

Provides annotated genomes of farmed and domesticated animals in an easily viewable format via the Ensembl system.

Provides access to genome-scale data from bacteria, protists, fungi, plants and invertebrate metazoa, through a unified set of interactive and programmatic interfaces based on the Ensembl software platform.

A Python framework for the analysis and visualization of trees.

ENZYME is a repository of information on enzyme nomenclature based on the recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology (NC-IUBMB). ENZYME describes each type of characterized enzyme for which an EC (Enzyme Commission) number has been provided.

An annotated non-redundant collection of eukaryotic POL II promoters, for which the transcription start site has been determined experimentally. Pointers to positions in nucleotide sequence entries provide access to promoter sequences. 

European Search Catalogue for Plant Genetic Resources, information about 1.9 million accessions of crop plants and their wild relatives, preserved ex situ by almost 400 institutes.

The European Genome-phenome Archive (EGA) allows users to explore datasets from numerous genotype experiments, including case-control, population and family studies, that are supplied by a range of data providers. 

Europe PubMedCentral (EuropePMC) contains over 3 million full text life science research articles, of which over 900 000 are open access, and combines these with 30 million abstracts from PubMed and other sources. 

European Variation Archive

The Expression Atlas allows users to search for gene expression changes measured in various cell types, organism parts, and disease states. It represents a curated subset of the ArrayExpress and GEO Archive experiments.

A visualization tool for positional annotations on a sequence

Federated service for permanent archiving and sharing of all types of personally identifiable genetic and phenotypic data resulting from biomedical research projects

A worldwide database documenting the prevalence of clinically relevant genome variation allele frequencies in populations worldwide

FireProtDB is a comprehensive, manually curated database of the protein stability data for single-point mutants. Proteins find their use in numerous biomedical and biotechnological applications. Naturally occurring proteins usually cannot withstand harsh industrial environments since they have evolved to function under mild conditions. Increasing protein stability is one of the key determinants of protein applicability. The predictive power of the current computational tools is compromised by the limited experimental data that would allow a rigorous training and testing.

Database and web portal for genetic and genomic information on fruit fly Drosophila melanogaster and related fly species.

A database of structural features for three galactose metabolism enzymes (GALT, GALK, GALE).