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Found 39 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

DNASU plasmid repository

DNASU

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DNASU is a central repository for plasmid clones and collections. Currently we store and distribute over 200,000 plasmids including 75,000 human and mouse plasmids, full genome collections, the protein expression plasmids from the Protein Structure Initiative as the PSI: Biology Material Repository (PSI : Biology-MR), and both small and large collections from individual researchers. We are also a founding member and distributor of the ORFeome Collaboration plasmid collection.

Autism Chromosome Rearrangement Database

ACRD

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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breakpoints and other genomic features, related to autism, taken from publicly available literature: databases and unpublished data. The database is continuously updated with information from in-house experimental data as well as data from published research studies.

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.

NCBI Datasets

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NCBI Datasets is a continually evolving platform designed to provide easy and intuitive access to NCBI’s sequence data and metadata. NCBI Datasets is part of the NIH Comparative Genomics Resource (CGR). CGR facilitates reliable comparative genomics analyses for all eukaryotic organisms through an NCBI Toolkit and community collaboration.

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 >>>!!!>>>

Human Genetic Variation Repository

HGVD

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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 variations determined by exome sequencing of 1,208 individuals and genotyping data of common variations obtained from a cohort of 3,248 individuals.

Cancer GenomeAtlas Data Portal

Cancer Genome Atlas Data Portal

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The Cancer Genome Atlas (TCGA) Data Portal provides a platform for researchers to search, download, and analyze data sets generated by TCGA. It contains clinical information, genomic characterization data, and high level sequence analysis of the tumor genomes. The Data Coordinating Center (DCC) is the central provider of TCGA data. The DCC standardizes data formats and validates submitted data.

Clinical Genomic Database

CGD

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

Viral Bioinformatics Resource Center

VBRC

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

Cystic Fibrosis Mutation Database

CFTR1

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The Cystic Fibrosis Mutation Database (CFTR1) was initiated by the Cystic Fibrosis Genetic Analysis Consortium in 1989 to increase and facilitate communications among CF researchers, and is maintained by the Cystic Fibrosis Centre at the Hospital for Sick Children in Toronto. The specific aim of the database is to provide up to date information about individual mutations in the CFTR gene. In a major upgrade in 2010, all known CFTR mutations and sequence variants have been converted to the standard nomenclature recommended by the Human Genome Variation Society.

Bacterial and Viral Bioinformatics Resource Center

BV-BRC

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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.

BIGG Database

Biochemically, Genetically and Genomically structured genome-scale metabolic network reconstructions

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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.

GeneCards

The Human Gene Database

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GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

ALlele FREquency Database

ALFRED

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We are working on a new version of ALFRED web interface. The current web interface will not be available from December 15th, 2023. There will be a period where a public web interface is not available for viewing ALFRED data. Expected date for the deployment of the new ALFRED web interface with minimum functions is March 1st, 2024 --------------------------------------------- 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.

NCBI Genome

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<<<!!!<<< 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.

Gemma

Tools and database for meta-analysis of functional genomics data

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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.

GenomeRNAi

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GenomeRNAi is a database containing phenotypes from RNA interference (RNAi) screens in Drosophila and Homo sapiens. In addition, the database provides an updated resource of RNAi reagents and their predicted quality.

Cancer Genomics Hub

CGHub

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>>>>!!!!<<<< 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: https://gdc.nci.nih.gov/ >>>>!!!!<<<< 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.

Cancer Genome Anatomy Project

CGAP

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>>>!!!<<< 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 Genomics Cloud available at the following location: https://mitelmandatabase.isb-cgc.org >>>!!!<<<

Complete Genomics

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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 data formats provided from our sequencing service, and augment their own research with additional summaries of genomic variation across a panel of diverse individuals. The quality of these data sets is representative of what a customer can expect to receive for their own samples. This public genome repository comprises genome results from both our Standard Sequencing Service (69 standard, non-diseased samples) and the Cancer Sequencing Service (two matched tumor and normal sample pairs). In March 2013 Complete Genomics was acquired by BGI-Shenzhen , the world’s largest genomics services company. BGI is a company headquartered in Shenzhen, China that provides comprehensive sequencing and bioinformatics services for commercial science, medical, agricultural and environmental applications. Complete Genomics is now focused on building a new generation of high-throughput sequencing technology and developing new and exciting research, clinical and consumer applications.

NCBI dbVar

Database of genomic structural VARiation

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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 ***

Estonian Biocentre Free Data

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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.

GigaDB

GigaScience Database

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GigaDB primarily serves as a repository to host data and tools associated with articles published by GigaScience Press; GigaScience and GigaByte (both are online, open-access journals). GigaDB defines a dataset as a group of files (e.g., sequencing data, analyses, imaging files, software programs) that are related to and support a unit-of-work (article or study). GigaDB allows the integration of manuscript publication with supporting data and tools.

AnimalGenome.ORG

BioMart AnimalGenome.ORG

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