This search engine combs for information from over 30 major databases at NCBI, including PubMed, nucleic acids, amino acid sequences, expression data, PubChem (small molecules with biochemical functions), protein structure, sequenced genomes, and taxonomy. The search engine provides links to the search results, as well as to other related databases.

Database of three-dimensional structures of macromolecules that 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. * Macromolecular structures: The three-dimensional structures of biomolecules provide a wealth of information on their biological function and evolutionary relationships. The Molecular Modeling Database (MMDB), as part of the Entrez system, facilitates access to structure data by connecting them with associated literature, protein and nucleic acid sequences, chemicals, biomolecular interactions, and more. It is possible, for example, to find 3D structures for homologs of a protein of interest by following the Related Structure link in an Entrez Protein sequence record. * Conserved domains and protein classification: Conserved domains are functional units within a protein that act as building blocks in molecular evolution and recombine in various arrangements to make proteins with different functions. The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, in addition to NCBI-curated domains that use 3D-structure information explicitly to define domain boundaries and provide insights into sequence/structure/function relationships. * Small molecules and their biological activity: The PubChem project provides information on the biological activities of small molecules and is a component of NIH''''s Molecular Libraries Roadmap Initiative. PubChem includes three databases: PCSubstance, PCBioAssay, and PCCompound. The PubChem data are linked to other data types (illustrated example) in the Entrez system, making it possible, for example, to retrieve information about a compound and then Link to its biological activity data, retrieve 3D protein structures bound to the compound and interactively view their active sites, and find biosystems that include the compound as a component. * Biological Systems: A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. The NCBI BioSystems Database provides centralized access to biological pathways from several source databases and connects the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system. BioSystem records list and categorize components (illustrated example), such as the genes, proteins, and small molecules involved in a biological system. The companion FLink icon FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems.

THIS RESOURCE IS NO LONGER IN SERVICE, documented on March 19, 2012. Due to budgetary constraints, the National Center for Biotechnology Information (NCBI) has discontinued support for the NCBI GENSAT database, and it has been removed from the Entrez System. The Gene Expression Nervous System Atlas (GENSAT) project involves the large-scale creation of transgenic mouse lines expressing green fluorescent protein (GFP) reporter or Cre recombinase under control of the BAC promoter in specific neural and glial cell populations. BAC expression data for all the lines generated (over 1300 lines) are available in online, searchable databases (www.gensat.org and the Database of GENSAT BAC-Cre driver lines). If you have any specific questions, please feel free to contact us at info_at_ncbi.nlm.nih.gov The GENSAT project aims to map the expression of genes in the central nervous system of the mouse, using both in situ hybridization and transgenic mouse techniques. Search criteria include gene names, gene symbols, gene aliases and synonyms, mouse ages, and imaging protocols. Mouse ages are restricted to E10.5 (embryonic day 10.5), E15.5 (embryonic day 15.5), P7 (postnatal day 7), and Adult (adult). The project focuses on two techniques * Evaluation of unmodified mice lines for expression of a given gene using radiolabelled riboprobes and in-situ hybridization. * Creation of transgenic mice lines containing a BAC construct that expresses a marker gene in the same environment as the native gene

NCBI Datasets is a valuable resource that simplifies the process of gathering data from various NCBI databases. Whether you’re a researcher, scientist, or bioinformatician, NCBI Datasets provides an efficient way to access sequence information, annotations, and metadata for genes and genomes.

Database that provides access to biological systems and their component genes, proteins, and small molecules, as well as literature describing those biosystems and other related data throughout Entrez. A biosystem, or biological system, is a group of molecules that interact directly or indirectly, where the grouping is relevant to the characterization of living matter. BioSystem records list and categorize components, such as the genes, proteins, and small molecules involved in a biological system. The companion FLink tool, in turn, allows you to input a list of proteins, genes, or small molecules and retrieve a ranked list of biosystems. A number of databases provide diagrams showing the components and products of biological pathways along with corresponding annotations and links to literature. This database was developed as a complementary project to (1) serve as a centralized repository of data; (2) connect the biosystem records with associated literature, molecular, and chemical data throughout the Entrez system; and (3) facilitate computation on biosystems data. The NCBI BioSystems Database currently contains records from several source databases: KEGG, BioCyc (including its Tier 1 EcoCyc and MetaCyc databases, and its Tier 2 databases), Reactome, the National Cancer Institute's Pathway Interaction Database, WikiPathways, and Gene Ontology (GO). It includes several types of records such as pathways, structural complexes, and functional sets, and is desiged to accomodate other record types, such as diseases, as data become available. Through these collaborations, the BioSystems database facilitates access to, and provides the ability to compute on, a wide range of biosystems data. If you are interested in depositing data into the BioSystems database, please contact them.

Databases of protein sequences and 3D structures of proteins. 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.

The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such.

LinkOut is a service that allows you to link directly from PubMed and other NCBI databases to a wide range of information and services beyond the NCBI systems. LinkOut aims to facilitate access to relevant online resources in order to extend, clarify, and supplement information found in NCBI databases. Third parties can link directly from PubMed and other Entrez database records to relevant Web-accessible resources beyond the Entrez system. Includes full-text publications, biological databases, consumer health information and research tools.

Database developed to archive and distribute clinical data and results from studies that have investigated interaction of genotype and phenotype in humans. Database to archive and distribute results of studies including genome-wide association studies, medical sequencing, molecular diagnostic assays, and association between genotype and non-clinical traits.

An extensive collection of articles about NCBI databases, data models, and software.

Database of unannotated short single-read primarily genomic sequences from GenBank including random survey sequences clone-end sequences and exon-trapped sequences. The GSS division of GenBank is similar to the EST division, with the exception that most of the sequences are genomic in origin, rather than cDNA (mRNA). It should be noted that two classes (exon trapped products and gene trapped products) may be derived via a cDNA intermediate. Care should be taken when analyzing sequences from either of these classes, as a splicing event could have occurred and the sequence represented in the record may be interrupted when compared to genomic sequence. The GSS division contains (but is not limited to) the following types of data: * random single pass read genome survey sequences. * cosmid/BAC/YAC end sequences * exon trapped genomic sequences * Alu PCR sequences * transposon-tagged sequences Although dbGSS sequences are incorporated into the GSS Division of GenBank, annotation in dbGSS is more comprehensive and includes detailed information about the contributors, experimental conditions, and genetic map locations.

Comparison of the sequences of 26H3 ORFS with uncharacterized and characterized proteins available in the CAZy and NCBI databases.

Staphylococcus agnetis is an emerging pathogen in chickens but has been most commonly isolated from sub-clinical mastitis in bovines. Previous whole-genome analyses for known virulence genes failed to identify determinants for the switch from mild ductal infections in cattle to severe infections in poultry. We now report identification of a family of 15 kbp, 17–19 gene mobile genetic elements (MGEs) specific to chicken osteomyelitis and dermatitis isolates of S. agnetis. These MGEs can be present in multiple copies per genome. The MGE has been vectored on a Staphylococcus phage that separately lysogenized two S. agnetis osteomyelitis strains. The S. agnetis genome from a broiler breeder case of ulcerative dermatitis contains 2 orthologs of this MGE, not associated with a prophage. BLASTn and phylogenetic analyses show that there are closely related intact MGEs found in genomes of S. aureus. The genome from a 1980s isolate from chickens in Ireland contains 3 copies of this MGE. More recent chicken isolates descended from that genome (Poland 2009, Oklahoma 2010, and Arkansas 2018) contain 2 to 4 related copies. Many of the genes of this MGE can be identified in disparate regions of the genomes of other chicken isolates of S. aureus. BLAST searches of the NCBI databases detect no similar MGEs outside of S. aureus and S. agnetis. These MGEs encode no proteins related to those produced by Staphylococcus aureus Pathogenicity Islands, which have been associated with the transition of S. aureus from human to chicken hosts. Other than mobilization functions, most of the genes in these new MGEs annotate as hypothetical proteins. The MGEs we describe appear to represent a new family of Chromosomal Islands (CIs) shared amongst S. agnetis and S. aureus. Further work is needed to understand the role of these CIs/MGEs in pathogenesis. Analysis of horizontal transfer of genetic elements between isolates and species of Staphylococci provides clues to evolution of host-pathogen interactions as well as revealing critical determinants for animal welfare and human diseases.

A premier bibliographic database that contains over 18 million references to journal articles in life sciences with a concentration on biomedicine. A distinctive feature is that the records are indexed with NLM Medical Subject Headings (MeSH). PubMed provides free access to MEDLINE and links to full text articles when possible. The great majority of journals are selected for MEDLINE based on the recommendation of the Literature Selection Technical Review Committee (LSTRC), an NIH-chartered advisory committee of external experts analogous to the committees that review NIH grant applications. Some additional journals and newsletters are selected based on NLM-initiated reviews, e.g., history of medicine, health services research, AIDS, toxicology and environmental health, molecular biology, and complementary medicine, that are special priorities for NLM or other NIH components. These reviews generally also involve consultation with an array of NIH and outside experts or, in some cases, external organizations with which NLM has special collaborative arrangements. MEDLINE is the primary component of PubMed, part of the Entrez series of databases provided by the NLM National Center for Biotechnology Information (NCBI). MEDLINE may also be searched via the NLM Gateway. Time coverage: generally 1946 to the present, with some older material. Source: Currently, citations from approximately 5,516 worldwide journals in 39 languages; 60 languages for older journals. Citations for MEDLINE are created by the NLM, international partners, and collaborating organizations.

Comparison of the sequences of 36A23 ORFs with uncharacterized and characterized proteins available in the CAZy and NCBI databases.

Database of biological data related to a single initiative, originating from a single organization or from a consortium. A BioProject record provides users a single place to find links to the diverse data types generated for that project. It is a searchable collection of complete and incomplete (in-progress) large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms. Submissions are supported by a web-based Submission Portal. The database facilitates organization and classification of project data submitted to NCBI, EBI and DDBJ databases that captures descriptive information about research projects that result in high volume submissions to archival databases, ties together related data across multiple archives and serves as a central portal by which to inform users of data availability. BioProject records link to corresponding data stored in archival repositories. The BioProject resource is a redesigned, expanded, replacement of the NCBI Genome Project resource. The redesign adds tracking of several data elements including more precise information about a project''''s scope, material, and objectives. Genome Project identifiers are retained in the BioProject as the ID value for a record, and an Accession number has been added. Database content is exchanged with other members of the International Nucleotide Sequence Database Collaboration (INSDC). BioProject is accessible via FTP.

This database was built to identify taxa in metagenome samples using the CCMetagen pipeline. The whole NCBI nt collection allows a complete taxonomic overview, including from microbial eukaryotes that may be present in the dataset. This database is already indexed, ready to use with KMA and CCMetagen.

A manual describing how to use this dataset can be found at: https://github.com/vrmarcelino/CCMetagen

Additionally, a tutorial on the whole analysis of a set of metatranscriptome samples can be found at: https://github.com/vrmarcelino/CCMetagen/tree/master/tutorial

The database was built as follows:

The partially non-redundant nucleotide database was downloaded from the NCBI website (ftp://ftp.ncbi.nih.gov/blast/db/FASTA/nt.gz) in January 2018. This database was formatted to include taxids in sequence headers.

Indexing was then performed with KMA using the commands:

kma_index -i nt_taxid.fas -o ncbi_nt -NI -Sparse TG

Three indexed databases are provided:

1. NCBI nucleotide collection
2. RefSeq database of bacterial and fungal genomes

The NCBI Probe Database is a public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.

The gene database provides information on gene sequence, structure, location, and function for annotated genes from the NCBI database. Users can search by accession ID or keyword, compare and identify sequences using BLAST, or submit references into function (RIFs) based on experimental results. Bulk download and an update mailing list are available.

Database for a curated classification and nomenclature that contains the names of all organisms that are represented in the public sequence databases with at least one nucleotide or protein sequence. Data provided encompasses archaea, bacteria, eukaryota, viroids and viruses. The NCBI taxonomy database is not a primary source for taxonomic or phylogenetic information. Furthermore, the database does not follow a single taxonomic treatise but rather attempts to incorporate phylogenetic and taxonomic knowledge from a variety of sources, including the published literature, web-based databases, and the advice of sequence submitters and outside taxonomy experts. Consequently, the NCBI taxonomy database is not a phylogenetic or taxonomic authority and should not be cited as such.