Biology
Genetics
- BLASTThe Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
- GeneA searchable database of genes, focusing on genomes that have been completely sequenced and that have an active research community to contribute gene-specific data. Information includes nomenclature, chromosomal localization, gene products and their attributes (e.g., protein interactions), associated markers, phenotypes, interactions, and links to citations, sequences, variation details, maps, expression reports, homologs, protein domain content, and external databases.
- GenomeContains sequence and map data from the whole genomes of over 1000 organisms. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life (bacteria, archaea, and eukaryota) are represented, as well as many viruses, phages, viroids, plasmids, and organelles.
- Nucleotide DatabaseA collection of nucleotide sequences from several sources, including GenBank, RefSeq, the Third Party Annotation (TPA) database, and PDB. Searching the Nucleotide Database will yield available results from each of its component databases.
- BioProject (formerly Genome Project)A collection of genomics, functional genomics, and genetics studies and links to their resulting datasets. This resource describes project scope, material, and objectives and provides a mechanism to retrieve datasets that are often difficult to find due to inconsistent annotation, multiple independent submissions, and the varied nature of diverse data types which are often stored in different databases.
- Gene Expression Omnibus (GEO) DatabaseA public functional genomics data repository supporting MIAME-compliant data submissions. Array- and sequence-based data are accepted and tools are provided to help users query and download experiments and curated gene expression profiles.
- HomologeneA gene homology tool that compares nucleotide sequences between pairs of organisms in order to identify putative orthologs. Curated orthologs are incorporated from a variety of sources via the Gene database.
- Online Mendelian Inheritance in Man (OMIM)A database of human genes and genetic disorders.
- PopSetDatabase of related DNA sequences that originate from comparative studies: phylogenetic, population, environmental and, to a lesser degree, mutational. Each record in the database is a set of DNA sequences. For example, a population set provides information on genetic variation within an organism, while a phylogenetic set may contain sequences, and their alignment, of a single gene obtained from several related organisms.
- Trace ArchiveA repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects.
National Center for Biotechnology Information
The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. All information on the NCBI website is available to the public. Featured databases and tools are listed on this page. View the full list of resources.
- NCBI Education PageProvides links to tutorials and training materials, including PowerPoint slides and print handouts.
- NCBI HandbookAn extensive collection of articles about NCBI databases and software. Designed for a novice user, each article presents a general overview of the resource and its design, along with tips for searching and using available analysis tools. All articles can be searched online and downloaded in PDF format; the handbook can be accessed through the NCBI Bookshelf.
- NCBI Help ManualAccessed through the NCBI Bookshelf, the Help Manual contains documentation for many NCBI resources, including PubMed, PubMed Central, the Entrez system, Gene, SNP and LinkOut. All chapters can be downloaded in PDF format.
Genetics Home Reference
- Genetics Home ReferenceA consumer health website from the National Library of Medicine, which is part of the National Institutes of Health, an agency of the U.S. Department of Health and Human Services. The website provides information for the general public about the effects of genetic variation on human health.
Chemicals & Bioassays
- PubChem BioAssayConsists of deposited bioactivity data and descriptions of bioactivity assays used to screen the chemical substances contained in the PubChem Substance database, including descriptions of the conditions and the readouts (bioactivity levels) specific to the screening procedure.
- PubChem CompoundContains unique, validated chemical structures (small molecules) that can be searched using names, synonyms or keywords. The compound records may link to more than one PubChem Substance record if different depositors supplied the same structure. These Compound records reflect validated chemical depiction information provided to describe substances in PubChem Substance. Structures stored within PubChem Compounds are pre-clustered and cross-referenced by identity and similarity groups. Additionally, calculated properties and descriptors are available for searching and filtering of chemical structures.
- PubChem SubstancePubChem Substance records contain substance information electronically submitted to PubChem by depositors. This includes any chemical structure information submitted, as well as chemical names, comments, and links to the depositor's web site.
- PubChem Structure SearchPubChem Structure Search allows the PubChem Compound Database to be queried by chemical structure or chemical structure pattern. The PubChem Sketcher allows a query to be drawn manually. Users may also specify the structural query input by PubChem Compound Identifier (CID), SMILES, SMARTS, InChI, Molecular Formula, or by upload of a supported structure file format.
Proteins
- BLASTThe Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
- Conserved Domain Database (CDD)A collection of sequence alignments and profiles representing protein domains conserved in molecular evolution. It also includes alignments of the domains to known 3-dimensional protein structures in the MMDB database.
- Protein ClustersA collection of related protein sequences (clusters), consisting of Reference Sequence proteins encoded by complete prokaryotic and organelle plasmids and genomes. The database provides easy access to annotation information, publications, domains, structures, external links, and analysis tools.
- Protein DatabaseA database that includes protein sequence records from a variety of sources, including GenPept, RefSeq, Swiss-Prot, PIR, PRF, and PDB.
Variation
- Database of Genomic Structural Variation (dbVar)The dbVar database has been developed to archive information associated with large scale genomic variation, including large insertions, deletions, translocations and inversions. In addition to archiving variation discovery, dbVar also stores associations of defined variants with phenotype information.
- Database of Genotypes and Phenotypes (dbGaP)An archive and distribution center for the description and results of studies which investigate the interaction of genotype and phenotype. These studies include genome-wide association (GWAS), medical resequencing, molecular diagnostic assays, as well as association between genotype and non-clinical traits.
- Database of Short Genetic Variations (dbSNP)Includes single nucleotide variations, microsatellites, and small-scale insertions and deletions. dbSNP contains population-specific frequency and genotype data, experimental conditions, molecular context, and mapping information for both neutral variations and clinical mutations.
Literature
- MeSH DatabaseMeSH (Medical Subject Headings) is the U.S. National Library of Medicine's controlled vocabulary for indexing articles for MEDLINE/PubMed. MeSH terminology provides a consistent way to retrieve information that may use different terminology for the same concepts.
- BookshelfA collection of biomedical books that can be searched directly or from linked data in other NCBI databases. The collection includes biomedical textbooks, other scientific titles, genetic resources such as GeneReviews, and NCBI help manuals.
- Journals in NCBI DatabasesSubset of the NLM Catalog database providing information on journals that are referenced in NCBI database records, including PubMed abstracts. This subset can be searched using the journal title, MEDLINE or ISO abbreviation, ISSN, or the NLM Catalog ID.
- PubMed This link opens in a new windowProvides access to bibliographic information in Medline and other sources. (See the available Help Sheet). For full functionality, log in to your MyNCBI account..
- PubMed Central This link opens in a new windowPubMed Central® (PMC) is a free full-text archive of biomedical and life sciences journal literature at the U.S. National Institutes of Health's National Library of Medicine (NIH/NLM).
- PubMedLabsContains more than 30 million citations and abstracts of peer-reviewed biomedical literature. It does not include full-text journal articles; however, links to the full text are often present when available from other sources, such as the publisher's website or PubMed Central (PMC).
- Last Updated: May 23, 2025 12:07 PM
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