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Found 13 result(s)

Expressed Sequence Tags database

dbEST

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dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. Expressed Sequence Tags (ESTs) are short (usually about 300-500 bp), single-pass sequence reads from mRNA (cDNA). Typically they are produced in large batches. They represent a snapshot of genes expressed in a given tissue and/or at a given developmental stage. They are tags (some coding, others not) of expression for a given cDNA library. Most EST projects develop large numbers of sequences. These are commonly submitted to GenBank and dbEST as batches of dozens to thousands of entries, with a great deal of redundancy in the citation, submitter and library information. To improve the efficiency of the submission process for this type of data, we have designed a special streamlined submission process and data format. dbEST also includes sequences that are longer than the traditional ESTs, or are produced as single sequences or in small batches. Among these sequences are products of differential display experiments and RACE experiments. The thing that these sequences have in common with traditional ESTs, regardless of length, quality, or quantity, is that there is little information that can be annotated in the record. If a sequence is later characterized and annotated with biological features such as a coding region, 5'UTR, or 3'UTR, it should be submitted through the regular GenBank submissions procedure (via BankIt or Sequin), even if part of the sequence is already in dbEST. dbEST is reserved for single-pass reads. Assembled sequences should not be submitted to dbEST. GenBank will accept assembled EST submissions for the forthcoming TSA (Transcriptome Shotgun Assembly) division. The individual reads which make up the assembly should be submitted to dbEST, the Trace archive or the Short Read Archive (SRA) prior to the submission of the assemblies.

NCBI Structure

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The Structure database provides three-dimensional structures of macromolecules for a variety of research purposes and allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships.

Fungal Genetics Stock Center

FGSC

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The Fungal Genetics Stock Center has preserved and distributed strains of genetically characterized fungi since 1960. The collection includes over 20,000 accessioned strains of classical and genetically engineered mutants of key model, human, and plant pathogenic fungi. These materials are distributed as living stocks to researchers around the world.

CR-EST

The IPK Crop EST Database

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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.

Array Express

functional genomics data

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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 submitted directly to ArrayExpress and curated by a team of specialist biological curators. In the past (until 2018) datasets from the NCBI Gene Expression Omnibus database were imported on a weekly basis. Data is collected to MIAME and MINSEQE standards.

Sequence Read Archive

SRA

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The Sequence Read Archive stores the raw sequencing data from such sequencing platforms as the Roche 454 GS System, the Illumina Genome Analyzer, the Applied Biosystems SOLiD System, the Helicos Heliscope, and the Complete Genomics. It archives the sequencing data associated with RNA-Seq, ChIP-Seq, Genomic and Transcriptomic assemblies, and 16S ribosomal RNA data.

Protein Data Bank in Europe

PDBe

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PDBe is the European resource for the collection, organisation and dissemination of data on biological macromolecular structures. In collaboration with the other worldwide Protein Data Bank (wwPDB) partners - the Research Collaboratory for Structural Bioinformatics (RCSB) and BioMagResBank (BMRB) in the USA and the Protein Data Bank of Japan (PDBj) - we work to collate, maintain and provide access to the global repository of macromolecular structure data. We develop tools, services and resources to make structure-related data more accessible to the biomedical community.

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.

Finnish Biodiversity Information Facility

Laji.fi

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FinBIF is an integral part of the global biodiversity informatics framework, dedicated to managing species information. Its mission encompasses a wide array of services, including the generation of digital data through various processes, as well as the sourcing, collation, integration, and distribution of existing digital data. Key initiatives under FinBIF include the digitization of collections, the development of data systems for collections Kotka (https://biss.pensoft.net/article/37179/) and observations (https://biss.pensoft.net/article/39150/), and the establishment of a national DNA barcode reference library. FinBIF manages data types such as verbal species descriptions (which include drawings, pictures, and other media types), biological taxonomy, scientific collection specimens, opportunistic systematic and event-based observations, and DNA barcodes. It employs a unified IT architecture to manage data flows, delivers services through a single online portal, fosters collaboration under a cohesive umbrella concept, and articulates development visions under a unified brand. The portal Laji.fi serves as the entry point to this harmonized open data ecosystem. FinBIF's portal is accessible in Finnish, Swedish, and English. Data intended for restricted use are made available to authorities through a separate portal, while open data are also shared with international systems, such as GBIF.

Weed Images

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Weed Images is a project of the University of Georgia’s Center for Invasive Species and Ecosystem Health and one of the four major parts of BugwoodImages. The Focus is on damages of weed. It provides an easily accessible archive of high quality images for use in educational applications. In most cases, the images found in this system were taken by and loaned to us by photographers other than ourselves. Most are in the realm of public sector images. The photographs are in this system to be used.

NCBI Protein

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The Protein database is a collection of sequences from several sources, including translations from annotated coding regions in GenBank, RefSeq and TPA, as well as records from SwissProt, PIR, PRF, and PDB. Protein sequences are the fundamental determinants of biological structure and function.

NCBI Nucleotide

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The NCBI Nucleotide database collects sequences from such sources as GenBank, RefSeq, TPA, and PDB. Sequences collected relate to genome, gene, and transcript sequence data, and provide a foundation for research related to the biomedical field.

Alaska Ocean Observing System

AOOS

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Alaska Ocean Observing System (AOOS) provides ocean and coastal observations data. The AOOS is governed by the Integrated Ocean Observing System (IOOS) which is a partnership among federal, regional, academic and private sector groups. The Ocean Data Explorer contains scientific and management information including real-time sensor feeds, operational oceanographic and atmospheric models, satellite observations and GIS data sets that describe the biological, chemical and physical characteristics of Alaska and its surrounding waters. This map offers many new updated features that build upon the existing data system.