Database resources of the National Center for Biotechnology

Database resources of the National Center for Biotechnology

2003 | David L. Wheeler*, Deanna M. Church, Scott Federhen, Alex E. Lash, Thomas L. Madden, Joan U. Pontius, Gregory D. Schuler, Lynn M. Schriml, Edwin Sequeira, Tatiana A. Tatusova and Lukas Wagner
The National Center for Biotechnology Information (NCBI) provides a wide range of database resources and tools for the analysis and retrieval of biological data. These resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). These resources are accessible through the NCBI home page at http://www.ncbi.nlm.nih.gov. The NCBI was established in 1988 to develop information systems for molecular biology. It maintains the GenBank nucleic acid sequence database and provides data retrieval systems and computational resources for the analysis of GenBank data and other biological data. The NCBI suite of database resources is grouped into six categories. All resources are available from the NCBI home page. The data underlying these resources is available for bulk download at ftp.ncbi.nih.gov. The Entrez system is an integrated database retrieval system for DNA and protein sequences, as well as for genome maps, population sets, gene expression data, protein structures, and the biomedical literature. PubMed includes over 12 million references and abstracts in MEDLINE, with links to the full-text of over 3000 journals. The Books database now contains 12 online scientific textbooks. The NCBI taxonomy database indexes over 119,000 organisms. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group. The Entrez Taxonomy system allows for the display of custom taxonomic trees. LocusLink offers a single query interface to curated sequences and descriptive information about genes, including links to NCBI's Map Viewer, Evidence Viewer, Model Maker, BLAST Link, protein domains from the Conserved Domain Database, and many other gene-related resources. The BLAST family of sequence-similarity search programs, including BLAST, BLAST2Sequences, and MegaBLAST, are used for sequence similarity searches against various sequence databases. BLAST returns a set of gapped alignments between the query and similar database sequences, with links to the full database records and to other relevant databases. MegaBLAST is designed to search for nearlyThe National Center for Biotechnology Information (NCBI) provides a wide range of database resources and tools for the analysis and retrieval of biological data. These resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBI Taxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). These resources are accessible through the NCBI home page at http://www.ncbi.nlm.nih.gov. The NCBI was established in 1988 to develop information systems for molecular biology. It maintains the GenBank nucleic acid sequence database and provides data retrieval systems and computational resources for the analysis of GenBank data and other biological data. The NCBI suite of database resources is grouped into six categories. All resources are available from the NCBI home page. The data underlying these resources is available for bulk download at ftp.ncbi.nih.gov. The Entrez system is an integrated database retrieval system for DNA and protein sequences, as well as for genome maps, population sets, gene expression data, protein structures, and the biomedical literature. PubMed includes over 12 million references and abstracts in MEDLINE, with links to the full-text of over 3000 journals. The Books database now contains 12 online scientific textbooks. The NCBI taxonomy database indexes over 119,000 organisms. The Taxonomy Browser can be used to view the taxonomic position or retrieve sequence and structural data for a particular organism or group. The Entrez Taxonomy system allows for the display of custom taxonomic trees. LocusLink offers a single query interface to curated sequences and descriptive information about genes, including links to NCBI's Map Viewer, Evidence Viewer, Model Maker, BLAST Link, protein domains from the Conserved Domain Database, and many other gene-related resources. The BLAST family of sequence-similarity search programs, including BLAST, BLAST2Sequences, and MegaBLAST, are used for sequence similarity searches against various sequence databases. BLAST returns a set of gapped alignments between the query and similar database sequences, with links to the full database records and to other relevant databases. MegaBLAST is designed to search for nearly
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