DATABASE

NCBI - National Center for Biotechnology Information

It is one of the largest databases in bioinformatics and molecular biology, housing genome sequencing data in its GenBank and maintaining an index of biomedical research articles that it makes available in the PubMed Central and PubMed databases.

NCBI is comprised of several interconnected databases and tools, including:

• GenBank: A DNA sequence database that stores genomic sequence information from various organisms;

• PubMed: A database of scientific literature with journal articles and abstracts;

• BLAST: Sequence alignment tool for comparing a nucleotide or protein sequence with sequences stored in databases;

• Entrez: Search system that integrates information from different NCBI databases, allowing comprehensive queries.

Data sending and storage

Researchers can submit new genetic sequences, gene expression data, and other biological information to NCBI. This data will be selected and validated before being included in public databases. NCBI stores large volumes of biological data, including DNA sequences, RNA sequences, proteins, genetic variant information, and more. Data is organized into structured formats for easy access and analysis.

Access and Consultation

• User interface: offers several interfaces to access your databases. The best known include the web interface and APIs for programmatic access;

• Entrez: An integrated search system that allows users to search and retrieve information from different databases of the NCBI with a single query;

• BLAST: Tool to compare a sequence of nucleotides or proteins.

The NCBI provides a large collection of online resources of biological information and data, articles, citations, and abstracts published in life sciences journals.

Kegg - Kyoto Encyclopedia of Genes and Genomes

It is a database and a system of bioinformatics tools developed to integrate and analyze information about genes, genomes, and metabolic and signaling pathways.

Comprised of multiple interconnected databases and resources, including:

• KEGG Pathway: Contains maps of metabolic and signaling pathways that represent biochemical interactions and metabolic pathways within cells;

• KEGG Genes: Provides information about genes and their functions in different organisms, including the association of genes with metabolic pathways and biological processes;

• KEGG Enzyme: Provides information about enzymes, their reactions and their associations with metabolic pathways;

• KEGG Disease: Contains information about diseases and their relationships with genes and metabolic pathways;

• KEGG Drug: Provides information about drugs and their targets, as well as the metabolic pathways and biological processes they affect.

Data entry and storage

Data on new genes, enzymes, pathways and diseases are continually added to KEGG from scientific publications, research projects and external databases. KEGG integrates information from different sources, such as genomic sequences, gene expression data, and scientific literature, to create a comprehensive, interconnected resource.

Access and Consultation

The web interface allows users to search and explore data about genes, enzymes, metabolic pathways and other components. Users can access pathway maps, view relationships between genes and enzymes, and obtain information about diseases and drugs.

KEGG offers APIs and command-line tools for programmatic data access and analysis. This allows KEGG to be integrated with other systems and to automate analysis.

Support

KEGG provides documentation and tutorials to help users understand how to use its tools and interpret data.

KEGG is a database designed to facilitate understanding of the functions and usefulness of complex biological systems, based on information at the molecular level. It integrates large-scale molecular datasets generated by genome sequencing and other high-throughput techniques.

UniProt - Universal Protein Resource

Is one of the most comprehensive and widely used databases for protein information. It offers a vast collection of data on protein sequences, their functions, structures and functional observations.

It is made up of three main database components:

• UniProtKB (UniProt Knowledgebase): The leading database of protein sequences and functional annotations. It is divided into two bottles:

  • • UniProtKB/Swiss-Prot: Contains high-quality, manually curated annotated entries. These entries contain information provided about protein functions, locations, interactions, and variants;

    • UniProtKB/TrEMBL: Includes entries based on automatic predictions and less planned annotations from genomic sequences not manually reviewed;

• UniParc (UniProt Archive): Stores all known protein sequences and their versions, allowing historical tracking of sequence changes;

• UniRef (UniProt Reference Clusters): Groups similar protein sequences into clusters to facilitate comparison and analysis. There are three levels of UniRef:

• UniRef100: Contains all protein sequences from UniProtKB and other sources, grouped by similarity;

• UniRef90: Groups together protein sequences with at least 90% similarity, regardless of species;

• UniRef50: Groups sequences with at least 50% similarity.

Data sending and storage

New protein sequences and associated information are submitted to UniProt through genomic sequencing initiatives, academic research and scientific publications. Data is curated and annotated to ensure quality and accuracy. UniProt performs manual curation to provide detailed and accurate annotations for entries in UniProtKB/Swiss-Prot. This includes scientific literature review, experimental validation and incorporation of data from different sources.

Access and Consultations 

Features an intuitive web interface that allows users to search and explore protein data. UniProt offers APIs and command-line tools for programmatic access and integration with other systems.

Analysis and visualization

UniProt entries include information on protein functions, subcellular localizations, post-translational modifications, interactions with other proteins, and genetic variants. It also offers tools to visualize protein structure, functional domains and interaction maps.

UniProt is the leading global resource for high-quality protein sequences and functional information, offering a comprehensive, freely accessible database. It provides tools for analyzing and comparing sequences, supporting research in molecular biology, biochemistry and biotechnology.