The NCBI houses a series of databases relevant tobiotechnology andbiomedicine and is an important resource for bioinformatics tools and services. Major databases includeGenBank for DNA sequences andPubMed, a bibliographic database for biomedical literature. Other databases include theNCBI Epigenomics database. All these databases are available online through theEntrez search engine. NCBI was directed byDavid Lipman,[2] one of the original authors of theBLAST sequence alignment program[3] and a widely respected figure inbioinformatics.
Since 1992, NCBI has grown to provide other databases in addition to GenBank. NCBI provides the Gene database,Online Mendelian Inheritance in Man, the Molecular Modeling Database (3D protein structures),dbSNP (a database ofsingle-nucleotide polymorphisms), the Reference Sequence Collection, a map of thehuman genome, and ataxonomy browser, and coordinates with the National Cancer Institute to provide the Cancer Genome Anatomy Project. The NCBI assigns a unique identifier (taxonomy ID number) to each species of organism.[5]
The NCBI has software tools that are available through web browsers or byFTP. For example,BLAST is a sequence similarity searching program. BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds.
The NCBI Bookshelf[6] is a collection of freely accessible, downloadable, online versions of selected biomedical books. The Bookshelf covers a wide range of topics includingmolecular biology,biochemistry,cell biology,genetics,microbiology, disease states from a molecular and cellular point of view, research methods, andvirology. Some of the books are online versions of previously published books, while others, such asCoffee Break, are written and edited by NCBI staff. The Bookshelf is a complement to theEntrez PubMed repository ofpeer-reviewed publication abstracts in that Bookshelf contents provide established perspectives on evolving areas of study and a context in which many disparate individual pieces of reported research can be organized.[citation needed]
BLAST is an algorithm used for calculating sequence similarity between biological sequences, such as nucleotide sequences ofDNA andamino acid sequences of proteins.[7] BLAST is a powerful tool for finding sequences similar to the query sequence within the same organism or in different organisms. It searches the query sequence on NCBI databases and servers and posts the results back to the person's browser in the chosen format. Input sequences to the BLAST are mostly in FASTA or GenBank format while output could be delivered in a variety of formats such as HTML, XML formatting, and plain text. HTML is the default output format for NCBI's web-page. Results for NCBI-BLAST are presented in graphical format with all the hits found, a table with sequence identifiers for the hits having scoring related data, along with the alignments for the sequence of interest and the hits received with analogous BLAST scores for these.[8]
TheEntrez Global Query Cross-Database Search System is used at NCBI for all the major databases such as Nucleotide and Protein Sequences, Protein Structures, PubMed, Taxonomy, Complete Genomes, OMIM, and several others.[9] Entrez is both an indexing and retrieval system having data from various sources for biomedical research. NCBI distributed the first version of Entrez in 1991, composed of nucleotide sequences fromPDB andGenBank, protein sequences from SWISS-PROT, translated GenBank, PIR, PRF, PDB, and associated abstracts and citations from PubMed. Entrez is specially designed to integrate the data from several different sources, databases, and formats into a uniform information model and retrieval system which can efficiently retrieve that relevant references, sequences, and structures.[10]
Gene has been implemented at NCBI to characterize and organize the information about genes. It serves as a major node in the nexus of the genomic map, expression, sequence, protein function, structure, and homology data. A unique GeneID is assigned to each gene record that can be followed through revision cycles.Gene records for known or predicted genes are established here and are demarcated by map positions or nucleotide sequences. Gene has several advantages over its predecessor, LocusLink, including, better integration with other databases in NCBI, broader taxonomic scope, and enhanced options for query and retrieval provided by the Entrez system.[11]
Protein database maintains the text record for individual protein sequences, derived from many different resources such as NCBI Reference Sequence (RefSeq) project, GenBank, PDB, and UniProtKB/SWISS-Prot. Protein records are present in different formats including FASTA andXML and are linked to other NCBI resources. Protein provides the relevant data to the users such as genes, DNA/RNA sequences, biological pathways, expression and variation data, and literature. It also provides the predetermined sets of similar and identical proteins for each sequence as computed by the BLAST. The Structure database of NCBI contains 3D coordinate sets for experimentally-determined structures in PDB that are imported by NCBI.The Conserved Domain database (CDD) of protein contains sequence profiles that characterize highly conserved domains within protein sequences. It also has records from external resources like SMART andPfam.There is another database of proteins known as Protein Clusters database, which contains sets of proteins sequences that are clustered according to the maximum alignments between the individual sequences as calculated by BLAST.[12]
PubChem database of NCBI is a public resource for molecules and their activities against biological assays. PubChem is searchable and accessible byEntrez information retrieval system.[13]
^NCBI Resource Coordinators (2012). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research 41 (Database issue): D8–D20.
^Ostell J. (2002). The NCBI Handbook, 2nd edition, Chapter 15, The Entrez Search and Retrieval System
^Maglott D.,Pruitt K. & Tatusova T. (2005). The NCBI Handbook, 2nd edition, Chapter 19, Gene: A Directory of Genes
^Sayers E. (2013). The NCBI Handbook, 2nd edition, NCBI Protein Resources
^Wang Y. & Bryant S H. (2014). The NCBI Handbook, 2nd edition, NCBI PubChem BioAssay Database
