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NCBI Tutorial
NCBI Tutorial
Published: 2014/03/29
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NCBI Gene Database - Overview
NCBI Gene Database - Overview
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using NCBI to build phylogenetic trees
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NCBI NOW, Lecture 5, More DNA-seq and Basic Variant Analysis
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Channel: NCBI
Bioinformatics lecture 16 primer design
Bioinformatics lecture 16 primer design
Published: 2014/06/26
Channel: Shomu's Biology
Using NCBI for Primer Design
Using NCBI for Primer Design
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Channel: srlab
Introduction to NCBI
Introduction to NCBI
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Obtain cDNA sequence for a gene using NCBI/ الحصول على تسلسل الحمض النووي التكميلي لجين معين
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NCBI Blast Tutorial
NCBI Blast Tutorial
Published: 2010/07/30
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NCBI
NCBI's Molecular Databases: An Introduction
Published: 2014/08/25
Channel: Medical College of Wisconsin Libraries
How to Use NCBI Blast
How to Use NCBI Blast
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Channel: Howcast
NCBI Blast search tutorial
NCBI Blast search tutorial
Published: 2009/11/17
Channel: Mason Posner
Webinar: NCBI Human Variation and Medical Genetics Resources
Webinar: NCBI Human Variation and Medical Genetics Resources
Published: 2016/05/31
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Obtain Genomic Sequence for a Gene
Obtain Genomic Sequence for a Gene
Published: 2012/05/23
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My Bibliography
My Bibliography
Published: 2012/01/13
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NCBI Minute: Finding Genes in PubMed
NCBI Minute: Finding Genes in PubMed
Published: 2015/12/07
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1. Búsqueda de secuencias genéticas en NCBI
1. Búsqueda de secuencias genéticas en NCBI
Published: 2013/05/29
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Webinar: Introduction to NCBI
Webinar: Introduction to NCBI's E-utilities API
Published: 2014/11/14
Channel: NCBI
Bioinformatics Practical 1 database searching and retrival of sequence
Bioinformatics Practical 1 database searching and retrival of sequence
Published: 2013/10/30
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NCBI nucleotide database, reading record, Bio125, 2015 spring
NCBI nucleotide database, reading record, Bio125, 2015 spring
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NCBI PubMed Tutorial
NCBI PubMed Tutorial
Published: 2010/02/05
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Webinar: A Practical Guide to NCBI BLAST on the Web
Webinar: A Practical Guide to NCBI BLAST on the Web
Published: 2015/04/14
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NCBI Database Intro
NCBI Database Intro
Published: 2014/12/12
Channel: profbiot
How to Use NCBI Database
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Published: 2010/09/07
Channel: Howcast
Explore Gene Pages at NCBI: Variation & Expression
Explore Gene Pages at NCBI: Variation & Expression
Published: 2015/11/18
Channel: NCBI
NCBI Minute: How to Submit Your 16S rRNA Data to NCBI
NCBI Minute: How to Submit Your 16S rRNA Data to NCBI
Published: 2017/03/31
Channel: NCBI
Bioinformatics practical 2 how to run NCBI  BLAST
Bioinformatics practical 2 how to run NCBI BLAST
Published: 2013/10/30
Channel: Shomu's Biology
Creating Phylogenetic Trees Using NCBI & MEGA
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Published: 2016/07/25
Channel: Lisa Sorlie
Webinar: A Submitter
Webinar: A Submitter's Guide to GenBank, Part 1
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Channel: NCBI
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Channel: Tayyaba Qamar
NCBI NOW, Lecture 1, NCBI Resources for NGS
NCBI NOW, Lecture 1, NCBI Resources for NGS
Published: 2015/11/24
Channel: NCBI
NCBI Minute:  Download Genome Data via FTP
NCBI Minute: Download Genome Data via FTP
Published: 2016/09/06
Channel: NCBI
NCBI 20th Anniversary Video
NCBI 20th Anniversary Video
Published: 2010/05/19
Channel: NCBI
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Published: 2015/05/08
Channel: NCBI
The Variation Viewer
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Published: 2014/05/15
Channel: NCBI
NCBI NOW, Lecture 7, Using BLAST for Genomic Analysis
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Published: 2016/02/11
Channel: NCBI
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Published: 2015/08/11
Channel: NCBI
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Webinar: A Practical Guide to NCBI BLAST
Published: 2016/05/17
Channel: NCBI
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Channel: Sebastiaan Bol
NCBI: Retrieve Sequences for an Organism
NCBI: Retrieve Sequences for an Organism
Published: 2010/05/24
Channel: NCBI
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My NCBI Track Collections: Introduction
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Channel: NCBI
The NCBI Minute: BioProject
The NCBI Minute: BioProject
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Channel: NCBI
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Sequence Viewer: Download Transcripts, Exons and Proteins
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Channel: NCBI
NCBI: Download a custom set of records
NCBI: Download a custom set of records
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Channel: NCBI
Need the Full Text Article?
Need the Full Text Article?
Published: 2013/04/24
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WIKIPEDIA ARTICLE

From Wikipedia, the free encyclopedia
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National Center for Biotechnology Information logo

The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). The NCBI is located in Bethesda, Maryland and was founded in 1988 through legislation sponsored by Senator Claude Pepper.

The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for the biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine.

NCBI was directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in bioinformatics. He also leads an intramural research program, including groups led by Stephen Altschul (another BLAST co-author), David Landsman, Eugene Koonin (a prolific author on comparative genomics), John Wilbur, Teresa Przytycka, and Zhiyong Lu. David Lipman stood down from his post in May 2017.[1]

NCBI is listed in the Registry of Research Data Repositories re3data.org.[2]

GenBank[edit]

NCBI has had responsibility for making available the GenBank DNA sequence database since 1992.[3] GenBank coordinates with individual laboratories and other sequence databases such as those of the European Molecular Biology Laboratory (EMBL) and the DNA Data Bank of Japan (DDBJ).[4]

Since 1992, NCBI has grown to provide other databases in addition to GenBank. NCBI provides Gene, Online Mendelian Inheritance in Man, the Molecular Modeling Database (3D protein structures), dbSNP (a database of single-nucleotide polymorphisms), the Reference Sequence Collection, a map of the human genome, and a taxonomy 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 by WWW browsing or by FTP. For example, BLAST is a sequence similarity searching program. BLAST can do sequence comparisons against the GenBank DNA database in less than 15 seconds.

NCBI Bookshelf[edit]

The "NCBI Bookshelf[6] is a collection of freely accessible, downloadable, on-line versions of selected biomedical books. The Bookshelf covers a wide range of topics including molecular biology, biochemistry, cell biology, genetics, microbiology, disease states from a molecular and cellular point of view, research methods, and virology. Some of the books are online versions of previously published books, while others, such as Coffee Break, are written and edited by NCBI staff. The Bookshelf is a complement to the Entrez PubMed repository of peer-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]

Basic Local Alignment Search Tool (BLAST)[edit]

BLAST is an algorithm used for calculating sequence similarity between biological sequences such as nucleotide sequences of DNA and amino 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 post the results back to the person's browser in chosen format. Input sequences to the BLAST are mostly in FASTA or Genbank format while output could be delivered in 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]

Entrez[edit]

The Entrez 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 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 from PDB and GenBank, protein sequences from SWISS-PROT, translated GenBank, PIR, PRF and 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[edit]

Gene has been implemented at NCBI to characterize and organize the information about genes. It serves as a major node in the nexus of 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 sequence. 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 Entrez system.[11]

Protein[edit]

Protein database is an important protein resource at NCBI. It maintains the text record for individual protein sequences, derived from many different resources such as NCBI Reference Sequence (RefSeq) project, GenbBank, PDB and UniProtKB/SWISS-Prot. Protein records are present in different formats including FASTA and XML 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 pre-determined 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 and Pfam. There is another database in protein 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 BioAssay database[edit]

PubChem BioAssay database of NCBI is a public resource for biological tests of small molecules and siRNA reagents. The major purpose of PubChem repository is to provide easy and free of cost access to all deposited data, and to provide intuitive data analysis tools. It is structured as a set of relational databases organized on Microsoft SQL servers. PubChem’s BioAssay data is searchable and accessible by Entrez information retrieval system. PubChem database provides programmatic and Web-based tools for users to search, review, and download a publications, bioactivity data for a compound, a BioAssay record, a molecular target.[13]

See also[edit]

Notes and references[edit]

  1. ^ "National Library of Medicine Announces Departure of NCBI Director Dr. David Lipman". www.nlm.nih.gov. Retrieved 2017-05-06. 
  2. ^ "NCBI Entry in re3data.org". www.re3data.org. Retrieved 21 August 2014. 
  3. ^ Mizrachi, Ilene (22 August 2007). "GenBank: The Nucleotide Sequence Database". National Center for Biotechnology Information (US) – via www.ncbi.nlm.nih.gov. 
  4. ^ Mizrachi, Ilene (22 August 2007). "GenBank: The Nucleotide Sequence Database". National Center for Biotechnology Information (US) – via www.ncbi.nlm.nih.gov. 
  5. ^ "Home - Taxonomy - NCBI". www.ncbi.nlm.nih.gov. 
  6. ^ "https://www.ncbi.nlm.nih.gov/books
  7. ^ Altschul Stephen; Gish Warren; Miller Webb; Myers Eugene; Lipman David (1990). "Basic local alignment search tool". Journal of Molecular Biology. 215 (3): 403–410. PMID 2231712. doi:10.1016/s0022-2836(05)80360-2. 
  8. ^ Madden T. (2002). The NCBI handbook, 2nd edition, Chapter 16, The BLAST Sequence Analysis Tool
  9. ^ NCBI Resource Coordinators (2012). "Database resources of the National Center for Biotechnology Information". Nucleic Acids Research 41 (Database issue): D8–D20.
  10. ^ Ostell J. (2002). The NCBI handbook, 2nd edition, Chapter 15, The Entrez Search and Retrieval System
  11. ^ Maglott D. Pruitt K. & Tatusova T. (2005). The NCBI handbook, 2nd edition, Chapter 19, Gene: A Directory of Genes
  12. ^ Sayers E. (2013). The NCBI handbook, 2nd edition, NCBI Protein Resources
  13. ^ Wang Y. & Bryant S H. (2014). The NCBI handbook, 2nd edition, NCBI PubChem BioAssay Database


External links[edit]

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