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<meta name="robots" content="NOINDEX,NOFOLLOW,NOARCHIVE,NOIMAGEINDEX" /><meta name="author" content="Jo McEntyre, Jim Ostell" /><meta name="citation_title" content="The NCBI Handbook" /><meta name="citation_publisher" content="National Center for Biotechnology Information (US)" /><meta name="citation_date" content="2002" /><meta name="citation_author" content="Jo McEntyre" /><meta name="citation_author" content="Jim Ostell" /><meta name="citation_fulltext_html_url" content="https://www.ncbi.nlm.nih.gov/books/NBK21101/" /><link rel="schema.DC" href="http://purl.org/DC/elements/1.0/" /><meta name="DC.Title" content="The NCBI Handbook" /><meta name="DC.Type" content="Text" /><meta name="DC.Publisher" content="National Center for Biotechnology Information (US)" /><meta name="DC.Contributor" content="Jo McEntyre" /><meta name="DC.Contributor" content="Jim Ostell" /><meta name="DC.Date" content="2002" /><meta name="DC.Identifier" content="https://www.ncbi.nlm.nih.gov/books/NBK21101/" /><meta name="description" content="Bioinformatics consists of a computational approach to biomedical information management and analysis. It is being used increasingly as a component of research within both academic and industrial settings and is becoming integrated into both undergraduate and postgraduate curricula. The new generation of biology graduates is emerging with experience in using bioinformatics resources and, in some cases, programming skills." /><meta name="og:title" content="The NCBI Handbook" /><meta name="og:type" content="book" /><meta name="og:description" content="Bioinformatics consists of a computational approach to biomedical information management and analysis. It is being used increasingly as a component of research within both academic and industrial settings and is becoming integrated into both undergraduate and postgraduate curricula. The new generation of biology graduates is emerging with experience in using bioinformatics resources and, in some cases, programming skills." /><meta name="og:url" content="https://www.ncbi.nlm.nih.gov/books/NBK21101/" /><meta name="og:site_name" content="NCBI Bookshelf" /><meta name="og:image" content="https://www.ncbi.nlm.nih.gov/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook-lrg.png" /><meta name="twitter:card" content="summary" /><meta name="twitter:site" content="@ncbibooks" /><meta name="warning" content="This publication is provided for historical reference only and the information may be out of date." /><meta name="bk-non-canon-loc" content="/books/n/handbook/toc/" /><link rel="canonical" href="https://www.ncbi.nlm.nih.gov/books/NBK21101/" /><link rel="stylesheet" href="/corehtml/pmc/css/figpopup.css" type="text/css" media="screen" /><link rel="stylesheet" href="/corehtml/pmc/css/bookshelf/2.26/css/books.min.css" type="text/css" /><link rel="stylesheet" href="/corehtml/pmc/css/bookshelf/2.26/css/books_print.min.css" type="text/css" /><style type="text/css">p a.figpopup{display:inline !important} .bk_tt {font-family: monospace} .first-line-outdent .bk_ref {display: inline} </style><script type="text/javascript" src="/corehtml/pmc/js/jquery.hoverIntent.min.js"> </script><script type="text/javascript" src="/corehtml/pmc/js/common.min.js?_=3.18"> </script><script type="text/javascript">window.name="mainwindow";</script><script type="text/javascript" src="/corehtml/pmc/js/bookshelf/2.26/book-toc.min.js"> </script><script type="text/javascript" src="/corehtml/pmc/js/bookshelf/2.26/books.min.js"> </script>
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<div class="pre-content"><div><div class="bk_prnt"><p class="small">NCBI Bookshelf. A service of the National Library of Medicine, National Institutes of Health.</p></div><div class="bk_msg_box bk_bttm_mrgn clearfix bk_noprnt"><div class="iconblock clearfix"><a class="img_link icnblk_img" title="Table of Contents Page" href="/books/n/handbook2e/"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook2e-lrg.png" alt="Cover" height="100px" width="80px" /></a><div class="icnblk_cntnt"><ul class="messages"><li class="info icon"><span class="icon"><a href="/books/n/handbook2e/">See "The NCBI Handbook, 2nd Edition"</a></span></li></ul></div></div></div><div class="messagearea bk_noprnt" style="margin-bottom:1.3846em "><ul class="messages"><li class="warn icon"><span class="icon">This publication is provided for historical reference only and the information may be out of date.</span></li></ul></div><div class="bk_prnt"><p style="color:red;"><strong>This publication is provided for historical reference only and the information may be out of date.</strong></p></div></div></div>
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<div class="main-content lit-style" itemscope="itemscope" itemtype="http://schema.org/Book"><div class="meta-content fm-sec"><div class="iconblock whole_rhythm clearfix no_top_margin"><a href="https://www.ncbi.nlm.nih.gov/" title="National Center for Biotechnology Information (US)" class="img_link icnblk_img" ref="pagearea=logo&targetsite=external&targetcat=link&targettype=publisher"><img class="source-thumb" src="/corehtml/pmc/pmcgifs/bookshelf/thumbs/th-handbook-lrg.png" alt="Cover of The NCBI Handbook" /></a><div class="icnblk_cntnt"><h1 id="_NBK21101_"><span itemprop="name">The NCBI Handbook</span></h1><div>Editors:</div><div class="contrib half_rhythm"><span itemprop="editor">Jo McEntyre</span></div><div class="contrib half_rhythm"><span itemprop="editor">Jim Ostell</span></div><div class="affiliation small">National Center for Biotechnology Information</div><div class="half_rhythm">Bethesda (MD): <a href="https://www.ncbi.nlm.nih.gov/" ref="pagearea=meta&targetsite=external&targetcat=link&targettype=publisher"><span itemprop="publisher">National Center for Biotechnology Information (US)</span></a>; <span itemprop="datePublished">2002</span>-.</div><div><a href="/books/about/copyright/">Copyright Notice</a></div></div></div></div><div class="body-content whole_rhythm" itemprop="text"><div itemprop="description"><p>Bioinformatics consists of a computational approach to biomedical information management
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and analysis. It is being used increasingly as a component of research within both
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academic and industrial settings and is becoming integrated into both undergraduate and
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postgraduate curricula. The new generation of biology graduates is emerging with
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experience in using bioinformatics resources and, in some cases, programming skills.</p><p>The National Center for Biotechnology Information (NCBI) is one of the world's premier
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Web sites for biomedical and bioinformatics research. Based within the National Library
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of Medicine at the National Institutes of Health, USA, the NCBI hosts many databases
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used by biomedical and research professionals. The services include PubMed, the
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bibliographic database; GenBank, the nucleotide sequence database; and the BLAST
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algorithm for sequence comparison, among many others.</p><p>Although each NCBI resource has online help documentation associated with it, there is no
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cohesive approach to describing the databases and search engines, nor any significant
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information on how the databases work or how they can be leveraged, for bioinformatics
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research on a larger scale. The NCBI Handbook is designed to address this information
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gap.</p><p>All of our users know how to execute a straightforward PubMed or BLAST search. However,
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feedback from help desk personnel and booth staff at scientific meetings suggests that
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people often want to know how to use our resources in a more sophisticated manner and
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are frequently unaware of less well-known databases that might be helpful to them. The
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intended audience for The NCBI Handbook is, therefore, the growing number of scientists
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and students who would like a more in-depth guide to NCBI resources—powerusers
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and aspiring powerusers.</p><p>The NCBI Handbook is focused on the relatively stable information about each resource; it
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is not a point-and-click user guide (this type of information can be found in the online
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help documents, referred to frequently but not repeated, in the Handbook). Each chapter
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is devoted to one service; after a brief overview on using the resource, there is an
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account of how the resource works, including topics such as how data are included in a
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database, database design, query processing, and how the different resources relate to
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each other. For example, the BLAST chapter briefly describes what to use BLAST for, the
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various varieties of the BLAST algorithm, and BLAST statistics, before discussing output
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formats, query processing, and tips for setting up a BLAST database. A certain amount of
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biological knowledge is assumed.</p><p>The online content will be updated when necessary, although major changes are not
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expected to occur more than once every few years. (For example, PubMed query processing
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does not change dramatically year after year.) We hope that The NCBI Handbook will
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provide a valuable reference for anyone who wants to use our resources more
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effectively.</p></div><div><h2>Contents</h2><ul id="toc_tllNBK21101_toc_Part1_bxml" class="simple-list toc toc-toggle"><li class="half_rhythm" id="toc_itm_NBK21101_toc_Part1_bxml"><a class="toc-item" href="/books/n/handbook/Part1.bxml/">Part 1. The Databases</a><ul id="toc_lst_NBK21101_toc_Part1_bxml" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1"><a class="toc-item" href="/books/n/handbook/ch1/">Chapter 1. GenBank: The Nucleotide Sequence Database</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch2"><a class="toc-item" href="/books/n/handbook/ch2/">Chapter 2. PubMed: The Bibliographic Database</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch3"><a class="toc-item" href="/books/n/handbook/ch3/">Chapter 3. Macromolecular Structure Databases</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch4"><a class="toc-item" href="/books/n/handbook/ch4/">Chapter 4. The Taxonomy Project</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch5"><a class="toc-item" href="/books/n/handbook/ch5/">Chapter 5. The Single Nucleotide Polymorphism Database (dbSNP) of Nucleotide Sequence Variation</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch6"><a class="toc-item" href="/books/n/handbook/ch6/">Chapter 6. The Gene Expression Omnibus (GEO): A Gene Expression and Hybridization Repository</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch7"><a class="toc-item" href="/books/n/handbook/ch7/">Chapter 7. Online Mendelian Inheritance in Man (OMIM): A Directory of Human Genes and Genetic Disorders</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch8"><a class="toc-item" href="/books/n/handbook/ch8/">Chapter 8. The NCBI BookShelf: Searchable Biomedical Books</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch9"><a class="toc-item" href="/books/n/handbook/ch9/">Chapter 9. PubMed Central (PMC): An Archive for Literature from Life Sciences Journals</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch10"><a class="toc-item" href="/books/n/handbook/ch10/">Chapter 10. The SKY/CGH Database for Spectral Karyotyping and Comparative Genomic Hybridization Data</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch11"><a class="toc-item" href="/books/n/handbook/ch11/">Chapter 11. The Major Histocompatibility Complex Database, dbMHC</a></li></ul></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_Part2_bxml"><a class="toc-item" href="/books/n/handbook/Part2.bxml/">Part 2. Data Flow and Processing</a><ul id="toc_lst_NBK21101_toc_Part2_bxml" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch12"><a class="toc-item" href="/books/n/handbook/ch12/">Chapter 12. Sequin: A Sequence Submission and Editing Tool</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch13"><a class="toc-item" href="/books/n/handbook/ch13/">Chapter 13. The Processing of Biological Sequence Data at NCBI</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch14"><a class="toc-item" href="/books/n/handbook/ch14/">Chapter 14. Genome Assembly and Annotation Process</a></li></ul></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_Part3_bxml"><a class="toc-item" href="/books/n/handbook/Part3.bxml/">Part 3. Querying and Linking the Data</a><ul id="toc_lst_NBK21101_toc_Part3_bxml" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch15"><a class="toc-item" href="/books/n/handbook/ch15/">Chapter 15. The Entrez Search and Retrieval System</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch16"><a class="toc-item" href="/books/n/handbook/ch16/">Chapter 16. The BLAST Sequence Analysis Tool</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch17"><a class="toc-item" href="/books/n/handbook/ch17/">Chapter 17. LinkOut: Linking to External Resources from Entrez Databases</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch18"><a class="toc-item" href="/books/n/handbook/ch18/">Chapter 18. The Reference Sequence (RefSeq) Database</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch19"><a class="toc-item" href="/books/n/handbook/ch19/">Chapter 19. Gene: A Directory of Genes</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch20"><a class="toc-item" href="/books/n/handbook/ch20/">Chapter 20. Using the Map Viewer to Explore Genomes</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch21"><a class="toc-item" href="/books/n/handbook/ch21/">Chapter 21. UniGene: A Unified View of the Transcriptome</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch22"><a class="toc-item" href="/books/n/handbook/ch22/">Chapter 22. The Clusters of Orthologous Groups (COGs) Database: Phylogenetic Classification of Proteins from Complete Genomes</a></li></ul></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_Part4_bxml"><a class="toc-item" href="/books/n/handbook/Part4.bxml/">Part 4. User Support</a><ul id="toc_lst_NBK21101_toc_Part4_bxml" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch23"><a class="toc-item" href="/books/n/handbook/ch23/">Chapter 23. User Services: Helping You Find Your Way</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch24"><a class="toc-item" href="/books/n/handbook/ch24/">Chapter 24. Exercises: Using Map Viewer</a></li></ul></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1237"><a class="toc-item" href="/books/n/handbook/A1237/">Glossary</a></li></ul></div></div></div>
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<div class="post-content"><div><div class="half_rhythm"><a href="/books/about/copyright/">Copyright Notice</a></div><div class="small"><span class="label">Bookshelf ID: NBK21101</span></div><div style="margin-top:2em" class="bk_noprnt"><div class="pagination bk_noprnt"><span class="inactive page_link prev">< Prev</span><a class="active page_link next" href="/books/n/handbook/Part1.bxml/" title="Next page in this title">Next ></a></div></div></div></div>
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