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Found 28 result(s)

ExPASy Bioinformatics Resource Portal

SIB Bioinformatics Resource Portal

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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 repositories and databases of SIB. For example: array map, MetaNetX, SWISS-MODEL and World-2DPAGE, and many others see a list here http://www.expasy.org/resources

NCBI Gene

Gene

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The Gene database provides detailed information for known and predicted genes defined by nucleotide sequence or map position. Gene supplies gene-specific connections in the nexus of map, sequence, expression, structure, function, citation, and homology data. Unique identifiers are assigned to genes with defining sequences, genes with known map positions, and genes inferred from phenotypic information. These gene identifiers are used throughout NCBI's databases and tracked through updates of annotation. Gene includes genomes represented by NCBI Reference Sequences (or RefSeqs) and is integrated for indexing and query and retrieval from NCBI's Entrez and E-Utilities systems.

DTU Bioinformatics

Center for Biological Sequence Analysis (formerly)

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

Ensembl Metazoa

e!EnsemblMetazoa

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Ensembl Metazoa is a genome-centric portal for metazoan species of scientific interest.

IntAct

IntAct Molecular Interaction Database

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IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.

AceView

AceView genes

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AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals’ transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated.

Copernicus Marine Environment Monitoring Service

CMEMS

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The Copernicus Marine Environment Monitoring Service (CMEMS) provides regular and systematic reference information on the physical and biogeochemical state, variability and dynamics of the ocean and marine ecosystems for the global ocean and the European regional seas. The observations and forecasts produced by the service support all marine applications, including: Marine safety; Marine resources; Coastal and marine environment; Weather, seasonal forecasting and climate. For instance, the provision of data on currents, winds and sea ice help to improve ship routing services, offshore operations or search and rescue operations, thus contributing to marine safety. The service also contributes to the protection and the sustainable management of living marine resources in particular for aquaculture, sustainable fisheries management or regional fishery organisations decision-making process. Physical and marine biogeochemical components are useful for water quality monitoring and pollution control. Sea level rise is a key indicator of climate change and helps to assess coastal erosion. Sea surface temperature elevation has direct consequences on marine ecosystems and appearance of tropical cyclones. As a result of this, the service supports a wide range of coastal and marine environment applications. Many of the data delivered by the service (e.g. temperature, salinity, sea level, currents, wind and sea ice) also play a crucial role in the domain of weather, climate and seasonal forecasting.

NCBI Probe

Probe

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<<<!!!<<< NCBI has retired the Probe Database >>>!!!>>>

RCSB Protein Data Bank

RCSB PDB

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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.

Cellular Phenotype database

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The Cellular Phenotype database stores data derived from high-throughput phenotypic studies and it is being developed as part of the Systems Microscopy Network of Excellence project. The aim of the Cellular Phenotype database is to provide easy access to phenotypic data and facilitate the integration of independent phenotypic studies. Through its interface, users can search for a gene of interest, or a collection of genes, and retrieve the loss-of-function phenotypes observed, in human cells, by suppressing the expression of the selected gene(s), through RNA interference (RNAi), across independent phenotypic studies. Similarly, users can search for a phenotype of interest and retrieve the RNAi reagents that have caused such phenotype and the associated target genes. Information about specific RNAi reagents can also be obtained when searching for a reagent ID.

dbSNP

SNV

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The NCBI Short Genetic Variations database, commonly known as dbSNP, catalogs short variations in nucleotide sequences from a wide range of organisms. These variations include single nucleotide variations, short nucleotide insertions and deletions, short tandem repeats and microsatellites. Short Genetic Variations may be common, thus representing true polymorphisms, or they may be rare. Some rare human entries have additional information associated withthem, including disease associations, genotype information and allele origin, as some variations are somatic rather than germline events. ***NCBI will phase out support for non-human organism data in dbSNP and dbVar beginning on September 1, 2017***

Physical mapping data at Canada's Michael Smith Genome Sciences Centre - Data

Physical Mapping Data Access

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FPC Mapping data files from species that have been fingerprinted at Canada's Michael Smith Genome Sciences Centre (BCGSC).

modENCODE

Model Organism ENCyclopedia of DNA Elements

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

ProteomeXchange

PX

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The ProteomeXchange consortium has been set up to provide a single point of submission of MS proteomics data to the main existing proteomics repositories, and to encourage the data exchange between them for optimal data dissemination. Current members accepting submissions are: The PRIDE PRoteomics IDEntifications database at the European Bioinformatics Institute focusing mainly on shotgun mass spectrometry proteomics data PeptideAtlas/PASSEL focusing on SRM/MRM datasets.

Electron Microscopy Data Bank

EMDB

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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.

Ensembl Bacteria

e!EnsemblBacteria

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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.

Ensembl Protists

e!EnsemblProtists

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EnsemblProtists is a genome-centric portal for protists species.

SOL Genomics Network

SGN

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The Sol Genomics Network (SGN) is a clade-oriented database dedicated to the biology of the Solanaceae family which includes a large number of closely related and many agronomically important species such as tomato, potato, tobacco, eggplant, pepper, and the ornamental Petunia hybrida. SGN is part of the International Solanaceae Initiative (SOL), which has the long-term goal of creating a network of resources and information to address key questions in plant adaptation and diversification

NCBI Epigenomics

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

Conserved Domain database

CDD

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The Conserved Domain Database is a resource for the annotation of functional units in proteins. Its collection of domain models includes a set curated by NCBI, which utilizes 3D structure to provide insights into sequence/structure/function relationships

Cassavabase

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Breeding, molecular, genetics and genomics data on cassava (Manihot esculenta) and wild relatives

PATRIC

Pathosystems Resource Integration Center

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<<<!!!<<< This repository is no longer available. >>>!!!>>> PATRIC will go offline by mid-December2022. Here is what you need to know. As announced previously, PATRIC, the bacterial BRC, and IRD / ViPR, the viral BRCs, are being merged into the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from these BRCs to provide an integrated resource for bacterial and viral genomics-based infectious disease research.

ALEXA

ALEXA-A

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ALEXA is a microarray design platform for 'alternative expression analysis'. This platform facilitates the design of expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, splicing and polyadenylation sites. We use the term 'ALEXA' to describe a collection of novel genomic methods for 'alternative expression' analysis. 'Alternative expression' refers to the identification and quantification of alternative mRNA transcripts produced by alternative transcript initiation, alternative splicing and alternative polyadenylation. This website provides supplementary materials, source code and other downloads for recent publications describing our studies of alternative expression (AE). Most recently we have developed a method, 'ALEXA-Seq' and associated resources for alternative expression analysis by massively parallel RNA sequencing.

ChEMBL

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ChEMBL is a database of bioactive drug-like small molecules, it contains 2-D structures, calculated properties (e.g. logP, Molecular Weight, Lipinski Parameters, etc.) and abstracted bioactivities (e.g. binding constants, pharmacology and ADMET data). The data is abstracted and curated from the primary scientific literature, and cover a significant fraction of the SAR and discovery of modern drugs We attempt to normalise the bioactivities into a uniform set of end-points and units where possible, and also to tag the links between a molecular target and a published assay with a set of varying confidence levels. Additional data on clinical progress of compounds is being integrated into ChEMBL at the current time.

THEMIS

Acceleration, Reconnection, Turbulence and Electrodynamics of the Moon’s Interaction with the Sun

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The THEMIS mission is a five-satellite Explorer mission whose primary objective is to understand the onset and macroscale evolution of magnetospheric substorms. The five small satellites were launched together on a Delta II rocket and they carry identical sets of instruments including an electric field instrument (EFI), a flux gate magnetometer (FGM), a search coil magnetometer (SCM), a electro-static analyzer, and solid state telescopes (SST). The mission consists of several phases. In the first phase, the spacecraft will all orbit as a tight cluster in the same orbital plane with apogee at 15.4 Earth radii (RE). In the second phase, also called the Dawn Phase, the satellites will be placed in their orbits and during this time their apogees will be on the dawn side of the magnetosphere. During the third phase (also known as the Tail Science Phase) the apogees will be in the magnetotail. The fourth phase is called the Dusk Phase or Radiation Belt Science Phase, with all apogees on the dusk side. In the fifth and final phase, the apogees will shift to the sunward side (Dayside Science Phase). The satellite data will be combined with observations of the aurora from a network of 20 ground observatories across the North American continent. The THEMIS-B (THEMIS-P1) and THEMIS-C (THEMIS-P2) were repurposed to study the lunar environment in 2009. The spacecraft were renamed ARTEMIS (Acceleration, Reconnection, Turbulence and Electrodynamics of the Moon’s Interaction with the Sun), with the P1 and P2 designations maintained.