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Found 33 result(s)

ASAP

A systematic annotation package for community analysis of genomes

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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.

Atlas of Living Australia

ALA

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The Atlas of Living Australia (ALA) combines and provides scientifically collected data from a wide range of sources such as museums, herbaria, community groups, government departments, individuals and universities. Data records consist of images, literature, molecular DNA data, identification keys, species interaction data, species profile data, nomenclature, source data, conservation indicators, and spatial data.

Barcode of Life Data Systems

BOLD Systems

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The Barcode of Life Data Systems (BOLD) provides DNA barcode data. BOLD's online workbench supports data validation, annotation, and publication for specimen, distributional, and molecular data. The platform consists of four main modules: a data portal, a database of barcode clusters, an educational portal, and a data collection workbench. BOLD is the go-to site for DNA-based identification. As the central informatics platform for DNA barcoding, BOLD plays a crucial role in assimilating and organizing data gathered by the international barcode research community. Two iBOL (International Barcode of Life) Working Groups are supporting the ongoing development of BOLD.

Brain Transcriptome Database

BrainTx

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The Brain Transcriptome Database (BrainTx) project aims to create an integrated platform to visualize and analyze our original transcriptome data and publicly accessible transcriptome data related to the genetics that underlie the development, function, and dysfunction stages and states of the brain.

Cancer Cell Line Encyclopedia

CCLE

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The Cancer Cell Line Encyclopedia project is a collaboration between the Broad Institute, and the Novartis Institutes for Biomedical Research and its Genomics Institute of the Novartis Research Foundation to conduct a detailed genetic and pharmacologic characterization of a large panel of human cancer models, to develop integrated computational analyses that link distinct pharmacologic vulnerabilities to genomic patterns and to translate cell line integrative genomics into cancer patient stratification. The CCLE provides public access to genomic data, analysis and visualization for about 1000 cell lines.

DNA Data Bank of Japan

DDBJ

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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.

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.

EMBL-EBI

European Molecular Biology Laboratory - European Bioinformatics Institute

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The European Bioinformatics Institute (EBI) has a long-standing mission to collect, organise and make available databases for biomolecular science. It makes available a collection of databases along with tools to search, download and analyse their content. These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular interactions and pathways. Connected to these are linking and descriptive data resources such as protein motifs, ontologies and many others. In many of these efforts, the EBI is a European node in global data-sharing agreements involving, for example, the USA and Japan.

ENCODE

Encyclopedia of DNA Elements

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The ENCODE Encyclopedia organizes the most salient analysis products into annotations, and provides tools to search and visualize them. The Encyclopedia has two levels of annotations: Integrative-level annotations integrate multiple types of experimental data and ground level annotations. Ground-level annotations are derived directly from the experimental data, typically produced by uniform processing pipelines.

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 Fungi

e!EnsemblFungi

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EnsemblFungi is a genome-centric portal for fungal species. It is a project to maintain annotation on selected genomes.

Ensembl Genomes

e!EnsemblGenomes

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The Ensembl genome annotation system, developed jointly by the EBI and the Wellcome Trust Sanger Institute, has been used for the annotation, analysis and display of vertebrate genomes since 2000. Since 2009, the Ensembl site has been complemented by the creation of five new sites, for bacteria, protists, fungi, plants and invertebrate metazoa, enabling users to use a single collection of (interactive and programatic) interfaces for accessing and comparing genome-scale data from species of scientific interest from across the taxonomy. In each domain, we aim to bring the integrative power of Ensembl tools for comparative analysis, data mining and visualisation across genomes of scientific interest, working in collaboration with scientific communities to improve and deepen genome annotation and interpretation.

Ensembl Metazoa

e!EnsemblMetazoa

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

Ensembl Plants

e!EnsemblPlants

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EnsemblPlants is a genome-centric portal for plant species. Ensembl Plants is developed in coordination with other plant genomics and bioinformatics groups via the EBI's role in the transPLANT consortium.

Ensembl Protists

e!EnsemblProtists

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EnsemblProtists is a genome-centric portal for protists species.

European Xenopus Resource Center

EXRC

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The European Xenopus Resource Centre (EXRC) is situated in Portsmouth, United Kingdom and provides tools and services to support researchers using Xenopus models. The EXRC depends on researchers to obtain and deposit Xenopus transgenic and mutant lines, Xenopus in-situ hybridization clones, Xenopus specific antibodies and other resources with the centre. EXRC staff perform quality assurance testing on these reagents and then makes them available to the community at cost. EXRC also supplies wild type Xenopus, embryos, oocytes, egg extracts, X.tropicalis Fosmids, X.laevis BACs and ORFeomes.

GenBank

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GenBank® is a comprehensive database that contains publicly available nucleotide sequences for almost 260 000 formally described species. These sequences are obtained primarily through submissions from individual laboratories and batch submissions from large-scale sequencing projects, including whole-genome shotgun (WGS) and environmental sampling projects. Most submissions are made using the web-based BankIt or standalone Sequin programs, and GenBank staff assigns accession numbers upon data receipt. Daily data exchange with the European Nucleotide Archive (ENA) and the DNA Data Bank of Japan (DDBJ) ensures worldwide coverage. GenBank is accessible through the NCBI Entrez retrieval system, which integrates data from the major DNA and protein sequence databases along with taxonomy, genome, mapping, protein structure and domain information, and the biomedical journal literature via PubMed. BLAST provides sequence similarity searches of GenBank and other sequence databases. Complete bimonthly releases and daily updates of the GenBank database are available by FTP.

Genome Sequence Archive

GSA

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GSA is a data repository specialized for archiving raw sequence reads. It supports data generated from a variety of sequencing platforms ranging from Sanger sequencing machines to single-cell sequencing machines and provides data storing and sharing services free of charge for worldwide scientific communities. In addition to raw sequencing data, GSA also accommodates secondary analyzed files in acceptable formats (like BAM, VCF). Its user-friendly web interfaces simplify data entry and submitted data are roughly organized as two parts, viz., Metadata and File, where the former can be further assorted into BioProject, BioSample, Experiment and Run, and the latter contains raw sequence reads.

Global Genome Biodiversity Network

DNA Bank Network (formerly)

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The DNA Bank Network was established in spring 2007 and was funded until 2011 by the German Research Foundation (DFG). The network was initiated by GBIF Germany (Global Biodiversity Information Facility). It offers a worldwide unique concept. DNA bank databases of all partners are linked and are accessible via a central web portal, providing DNA samples of complementary collections (microorganisms, protists, plants, algae, fungi and animals). The DNA Bank Network was one of the founders of the Global Genome Biodiversity Network (GGBN) and is fully merged with GGBN today. GGBN agreed on using the data model proposed by the DNA Bank Network. The Botanic Garden and Botanical Museum Berlin-Dahlem (BGBM) hosts the technical secretariat of GGBN and its virtual infrastructure. The main focus of the DNA Bank Network is to enhance taxonomic, systematic, genetic, conservation and evolutionary studies by providing: • high quality, long-term storage of DNA material on which molecular studies have been performed, so that results can be verified, extended, and complemented, • complete on-line documentation of each sample, including the provenance of the original material, the place of voucher deposit, information about DNA quality and extraction methodology, digital images of vouchers and links to published molecular data if available.

Greengenes

The Greengenes Database

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Greengenes is an Earth Sciences website that assists clinical and environmental microbiologists from around the globe in classifying microorganisms from their local environments. A 16S rRNA gene database addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies.

IPK Gatersleben

Leibniz Institute of Plant Genetics and Crop Plant Research

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The IPK stores a large volume of research results and information in various databases. The Institute of Plant Genetics and Crop Plant Research IPK Gatersleben, is a nonprofit research institution for crop genetics and molecular biology, and is part of the Leibniz Association. The mission of the IPK Gatersleben is to conduct basic and applied research in the area of plant genetics and crop plant research. The results of this work are not only of significant benefit to plant breeders and the agricultural industry, but also to the food, feed, and chemical industry. An additional research area, the use of renewable raw materials, is increasingly gaining in importance.

JGI MycoCosm

MycoCosm - the fungal genomics resource

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MycoCosm, the DOE JGI’s web-based fungal genomics resource, which integrates fungal genomics data and analytical tools for fungal biologists. It provides navigation through sequenced genomes, genome analysis in context of comparative genomics and genome-centric view. MycoCosm promotes user community participation in data submission, annotation and analysis.

National Wild Seed Resource Center

国家重要野生植物种质资源库

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The National Important Wild Plant Germplasm Repository has ten types of resources and data such as seeds, DNA, isolated materials, dried leaves, etc. totaling about 180,000 copies

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 PopSet

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NCBI PopSet collects DNA sequences to analyze the ways that populations are related by evolution. Such sequences indicate if populations originate from different members of the same species or from organisms of different species entirely.