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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meta name="warning" content="This publication is provided for historical reference only and the information may be out of date."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><div>Ilene Mizrachi.</div><div class="small">Created: October 9, 2002; Last Update: August 22, 2007.</div><ul id="toc_lst_NBK21101_toc_ch1" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_History"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.History">History</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_International_Collaboration"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.International_Collaboration">International Collaboration</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_Confidentiality_of_Data"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.Confidentiality_of_Data">Confidentiality of Data</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_Direct_Submissions"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.Direct_Submissions">Direct Submissions</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_Bulk_Submissions_HighThroughput_Geno"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.Bulk_Submissions_HighThroughput_Geno">Bulk Submissions: High-Throughput Genomic Sequence (HTGS)</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_Whole_Genome_Shotgun_Sequences_WGS"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.Whole_Genome_Shotgun_Sequences_WGS">Whole Genome Shotgun Sequences (WGS)</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_Bulk_Submissions_EST_STS_and_GSS"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.Bulk_Submissions_EST_STS_and_GSS">Bulk Submissions: EST, STS, and GSS</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_Bulk_Submissions_HTC_and_FLIC"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.Bulk_Submissions_HTC_and_FLIC">Bulk Submissions: HTC and FLIC</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_Submission_Tools"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.Submission_Tools">Submission Tools</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_Sequence_Data_Flow_and_Processing_Fr"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.Sequence_Data_Flow_and_Processing_Fr">Sequence Data Flow and Processing: From Laboratory to GenBank</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_Microbial_Genomes"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.Microbial_Genomes">Microbial Genomes</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_Third_Party_Annotation_TPA_Sequence"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.Third_Party_Annotation_TPA_Sequence">Third Party Annotation (TPA) Sequence Database</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_Appendix_GenBank_RefSeq_TPA_and_UniP"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.Appendix_GenBank_RefSeq_TPA_and_UniP">Appendix: GenBank, RefSeq, TPA and UniProt: What’s in a Name?</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch1_References"><a class="toc-item" href="/books/n/handbook/ch1/#ch1.References">References</a></li></ul></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><div>Kathi Canese, Jennifer Jentsch, and Carol Myers.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch2" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A43"><a class="toc-item" href="/books/n/handbook/ch2/#A43">Data Sources</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A47"><a class="toc-item" href="/books/n/handbook/ch2/#A47">Electronic Data Submission</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A49"><a class="toc-item" href="/books/n/handbook/ch2/#A49">Database Management and Hardware</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A50"><a class="toc-item" href="/books/n/handbook/ch2/#A50">Indexing</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A54"><a class="toc-item" href="/books/n/handbook/ch2/#A54">How PubMed Queries Are Processed</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A67"><a class="toc-item" href="/books/n/handbook/ch2/#A67">Using PubMed</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A76"><a class="toc-item" href="/books/n/handbook/ch2/#A76">Additional PubMed Features</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A83"><a class="toc-item" href="/books/n/handbook/ch2/#A83">Results</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A84"><a class="toc-item" href="/books/n/handbook/ch2/#A84">Links from PubMed</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A92"><a class="toc-item" href="/books/n/handbook/ch2/#A92">How to Create Hyperlinks to PubMed</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A93"><a class="toc-item" href="/books/n/handbook/ch2/#A93">Customer Support</a></li></ul></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><div>Eric Sayers and Steve Bryant.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch3" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A95"><a class="toc-item" href="/books/n/handbook/ch3/#A95">Overview</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A97"><a class="toc-item" href="/books/n/handbook/ch3/#A97">Content of the Molecular Modeling Database (MMDB)</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A110"><a class="toc-item" href="/books/n/handbook/ch3/#A110">Content of the Conserved Domain Database (CDD)</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A118"><a class="toc-item" href="/books/n/handbook/ch3/#A118">Finding and Viewing Structures</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A150"><a class="toc-item" href="/books/n/handbook/ch3/#A150">Finding and Viewing Structure Neighbors</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A178"><a class="toc-item" href="/books/n/handbook/ch3/#A178">Finding and Viewing Conserved Domains</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A202"><a class="toc-item" href="/books/n/handbook/ch3/#A202">Finding and Viewing Proteins with Similar Domain Architectures</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A213"><a class="toc-item" href="/books/n/handbook/ch3/#A213">Links Between Structure and Other Resources</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A222"><a class="toc-item" href="/books/n/handbook/ch3/#A222">Saving Output from Database Searches</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A226"><a class="toc-item" href="/books/n/handbook/ch3/#A226">FTP</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A231"><a class="toc-item" href="/books/n/handbook/ch3/#A231">Frequently Asked Questions</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A235"><a class="toc-item" href="/books/n/handbook/ch3/#A235">References</a></li></ul></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><div>Scott Federhen.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch4" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A247"><a class="toc-item" href="/books/n/handbook/ch4/#A247">Introduction</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A250"><a class="toc-item" href="/books/n/handbook/ch4/#A250">Adding to the Taxonomy Database</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A253"><a class="toc-item" href="/books/n/handbook/ch4/#A253">Using the Taxonomy Browser</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A267"><a class="toc-item" href="/books/n/handbook/ch4/#A267">The Taxonomy Database: TAXON</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A270"><a class="toc-item" href="/books/n/handbook/ch4/#A270">Nomenclature Issues</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1640"><a class="toc-item" href="/books/n/handbook/ch4/#A1640">Taxonomy in Entrez: A Quick Tour</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A282"><a class="toc-item" href="/books/n/handbook/ch4/#A282">The Common Tree Viewer</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A286"><a class="toc-item" href="/books/n/handbook/ch4/#A286">Indexing Taxonomy in Entrez</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A294"><a class="toc-item" href="/books/n/handbook/ch4/#A294">The Taxonomy Statistics Page</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A295"><a class="toc-item" href="/books/n/handbook/ch4/#A295">Other Relevant References</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A299"><a class="toc-item" href="/books/n/handbook/ch4/#A299">NCBI Taxonomists</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A300"><a class="toc-item" href="/books/n/handbook/ch4/#A300">Contact Us</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A301"><a class="toc-item" href="/books/n/handbook/ch4/#A301">Appendix 1. TAXON nametypes</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A317"><a class="toc-item" href="/books/n/handbook/ch4/#A317">Appendix 2. Functional classes of TAXON scientific names</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A331"><a class="toc-item" href="/books/n/handbook/ch4/#A331">Appendix 3. Other TAXON data types</a></li></ul></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><div>Adrienne Kitts and Stephen Sherry.</div><div class="small">Created: October 9, 2002; Last Update: February 2, 2011.</div><ul id="toc_lst_NBK21101_toc_ch5" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch5_ch5_s1"><a class="toc-item" href="/books/n/handbook/ch5/#ch5.ch5_s1">Introduction</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch5_ch5_s2"><a class="toc-item" href="/books/n/handbook/ch5/#ch5.ch5_s2">Searching dbSNP</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch5_ch5_s3"><a class="toc-item" href="/books/n/handbook/ch5/#ch5.ch5_s3">Submitted Content</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch5_ch5_s4"><a class="toc-item" href="/books/n/handbook/ch5/#ch5.ch5_s4">Computed Content (The dbSNP Build Cycle)</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch5_ch5_s5"><a class="toc-item" href="/books/n/handbook/ch5/#ch5.ch5_s5">dbSNP Resource Integration</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch5_ch5_s6"><a class="toc-item" href="/books/n/handbook/ch5/#ch5.ch5_s6">How to Create a Local Copy of dbSNP</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch5_ch5_s7"><a class="toc-item" href="/books/n/handbook/ch5/#ch5.ch5_s7">Appendix 1. dbSNP report formats.</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch5_ch5_s8"><a class="toc-item" href="/books/n/handbook/ch5/#ch5.ch5_s8">Appendix 2. Rules and methodology for mapping</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch5_Appendix_3_Alignment_profiling_funct"><a class="toc-item" href="/books/n/handbook/ch5/#ch5.Appendix_3_Alignment_profiling_funct">Appendix 3 Alignment profiling function</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch5_ch5_s9"><a class="toc-item" href="/books/n/handbook/ch5/#ch5.ch5_s9">Appendix 4. 3D structure neighbor analysis.</a></li></ul></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><div>Ron Edgar and Alex Lash.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch6" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A338"><a class="toc-item" href="/books/n/handbook/ch6/#A338">Site Description</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A339"><a class="toc-item" href="/books/n/handbook/ch6/#A339">Design and Implementation</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A343"><a class="toc-item" href="/books/n/handbook/ch6/#A343">Retrieving Data</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A353"><a class="toc-item" href="/books/n/handbook/ch6/#A353">Depositing Data</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A356"><a class="toc-item" href="/books/n/handbook/ch6/#A356">Search and Integration</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A359"><a class="toc-item" href="/books/n/handbook/ch6/#A359">Example of Retrieving Data</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A365"><a class="toc-item" href="/books/n/handbook/ch6/#A365">Future Directions</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A367"><a class="toc-item" href="/books/n/handbook/ch6/#A367">Frequently Asked Questions</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A394"><a class="toc-item" href="/books/n/handbook/ch6/#A394">Acknowledgments</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A395"><a class="toc-item" href="/books/n/handbook/ch6/#A395">Contributors</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A397"><a class="toc-item" href="/books/n/handbook/ch6/#A397">References</a></li></ul></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><div>Donna Maglott, Joanna S. Amberger, and Ada Hamosh.</div><div class="small">Created: October 9, 2002.</div><ul id="toc_lst_NBK21101_toc_ch7" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A407"><a class="toc-item" href="/books/n/handbook/ch7/#A407">Content and Access</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A413"><a class="toc-item" href="/books/n/handbook/ch7/#A413">Guide to OMIM Pages</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A419"><a class="toc-item" href="/books/n/handbook/ch7/#A419">FTP</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1756"><a class="toc-item" href="/books/n/handbook/ch7/#A1756">Legal Statement</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A420"><a class="toc-item" href="/books/n/handbook/ch7/#A420">References</a></li></ul></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><div>Bart Trawick, Jeff Beck, and Jo McEntyre.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch8" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A424"><a class="toc-item" href="/books/n/handbook/ch8/#A424">Content Acquisition</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A427"><a class="toc-item" href="/books/n/handbook/ch8/#A427">How to Use the Books</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A437"><a class="toc-item" href="/books/n/handbook/ch8/#A437">Technology</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A442"><a class="toc-item" href="/books/n/handbook/ch8/#A442">The BookShelf Data Flow</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A444"><a class="toc-item" href="/books/n/handbook/ch8/#A444">NCBI Book DTD</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A446"><a class="toc-item" href="/books/n/handbook/ch8/#A446">Frequently Asked Questions</a></li></ul></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><div>Jeff Beck and Ed Sequeira.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch9" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A458"><a class="toc-item" href="/books/n/handbook/ch9/#A458">A PubMed Central (PMC) Site Guide</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A466"><a class="toc-item" href="/books/n/handbook/ch9/#A466">Participation in PMC</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A467"><a class="toc-item" href="/books/n/handbook/ch9/#A467">Links to Other NCBI Resources</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A468"><a class="toc-item" href="/books/n/handbook/ch9/#A468">PMC Architecture</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A469"><a class="toc-item" href="/books/n/handbook/ch9/#A469">Data Flow: 1. SGML/XML Processing</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A482"><a class="toc-item" href="/books/n/handbook/ch9/#A482">Data Flow: 2. Loading the Database</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A488"><a class="toc-item" href="/books/n/handbook/ch9/#A488">Special Characters</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A490"><a class="toc-item" href="/books/n/handbook/ch9/#A490">PMC DTD</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A495"><a class="toc-item" href="/books/n/handbook/ch9/#A495">Frequently Asked Questions</a></li></ul></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><div>Turid Knutsen, Vasuki Gobu, Rodger Knaus, Thomas Ried, and Karl Sirotkin.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch10" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A500"><a class="toc-item" href="/books/n/handbook/ch10/#A500">Database Content</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A515"><a class="toc-item" href="/books/n/handbook/ch10/#A515">Data Analysis: Query Tools</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A519"><a class="toc-item" href="/books/n/handbook/ch10/#A519">Data Integration</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A522"><a class="toc-item" href="/books/n/handbook/ch10/#A522">Contributors</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A523"><a class="toc-item" href="/books/n/handbook/ch10/#A523">References</a></li></ul></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><div>Adrienne Kitts, Michael Feolo, and Wolfgang Helmberg.</div><div class="small">Created: May 27, 2003; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch11" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1783"><a class="toc-item" href="/books/n/handbook/ch11/#A1783">Introduction</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1784"><a class="toc-item" href="/books/n/handbook/ch11/#A1784">dbMHC Resources</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1876"><a class="toc-item" href="/books/n/handbook/ch11/#A1876">Database Content</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1889"><a class="toc-item" href="/books/n/handbook/ch11/#A1889">Integration with Other Resources</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1907"><a class="toc-item" href="/books/n/handbook/ch11/#A1907">References</a></li></ul></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><div>Jonathan Kans.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch12" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A539"><a class="toc-item" href="/books/n/handbook/ch12/#A539">Sequin: A Brief Overview</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A540"><a class="toc-item" href="/books/n/handbook/ch12/#A540">Sequence Submission</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A546"><a class="toc-item" href="/books/n/handbook/ch12/#A546">Packaging the Submissions</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A548"><a class="toc-item" href="/books/n/handbook/ch12/#A548">Viewing and Editing the Sequences</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A553"><a class="toc-item" href="/books/n/handbook/ch12/#A553">Computational Functions of Sequin</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A561"><a class="toc-item" href="/books/n/handbook/ch12/#A561">Advanced Topics</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1770"><a class="toc-item" href="/books/n/handbook/ch12/#A1770">Conclusion</a></li></ul></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><div>Karl Sirotkin, Tatiana Tatusova, Eugene Yaschenko, and Mark Cavanaugh.</div><div class="small">Created: October 9, 2002; Last Update: March 14, 2006.</div><ul id="toc_lst_NBK21101_toc_ch13" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch13_Overview"><a class="toc-item" href="/books/n/handbook/ch13/#ch13.Overview">Overview</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch13_Data_Flow_Components"><a class="toc-item" href="/books/n/handbook/ch13/#ch13.Data_Flow_Components">Data Flow Components</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch13_Data_Flow_Architectu"><a class="toc-item" href="/books/n/handbook/ch13/#ch13.Data_Flow_Architectu">Data Flow Architecture</a></li></ul></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><div>Paul Kitts.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch14" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1441"><a class="toc-item" href="/books/n/handbook/ch14/#A1441">Overview of the Genome Assembly and Annotation Process</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1447"><a class="toc-item" href="/books/n/handbook/ch14/#A1447">The Input Data</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1458"><a class="toc-item" href="/books/n/handbook/ch14/#A1458">Preparation of the Input Sequences</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1467"><a class="toc-item" href="/books/n/handbook/ch14/#A1467">Alignment of Sequences to the Input Genomic Sequences</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1473"><a class="toc-item" href="/books/n/handbook/ch14/#A1473">Genome Assembly</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1486"><a class="toc-item" href="/books/n/handbook/ch14/#A1486">Annotation of Genes</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1514"><a class="toc-item" href="/books/n/handbook/ch14/#A1514">Annotation of Other Features</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1519"><a class="toc-item" href="/books/n/handbook/ch14/#A1519">Product Data Sets</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1523"><a class="toc-item" href="/books/n/handbook/ch14/#A1523">Production of Maps That Display Genome Features</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1528"><a class="toc-item" href="/books/n/handbook/ch14/#A1528">Public Release of Assembly and Models</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1529"><a class="toc-item" href="/books/n/handbook/ch14/#A1529">Integration with Other Resources</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1534"><a class="toc-item" href="/books/n/handbook/ch14/#A1534">Contributors</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1535"><a class="toc-item" href="/books/n/handbook/ch14/#A1535">References</a></li></ul></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><div>Jim Ostell.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch15" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A589"><a class="toc-item" href="/books/n/handbook/ch15/#A589">Entrez Design Principles</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A597"><a class="toc-item" href="/books/n/handbook/ch15/#A597">Entrez Is a Discovery System</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A598"><a class="toc-item" href="/books/n/handbook/ch15/#A598">Entrez Is Growing</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A605"><a class="toc-item" href="/books/n/handbook/ch15/#A605">How Entrez Works</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A608"><a class="toc-item" href="/books/n/handbook/ch15/#A608">References</a></li></ul></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><div>Tom Madden.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch16" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A611"><a class="toc-item" href="/books/n/handbook/ch16/#A611">Introduction</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A612"><a class="toc-item" href="/books/n/handbook/ch16/#A612">How BLAST Works: The Basics</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A614"><a class="toc-item" href="/books/n/handbook/ch16/#A614">BLAST Scores and Statistics</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A615"><a class="toc-item" href="/books/n/handbook/ch16/#A615">BLAST Output: 1. The Traditional Report</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A620"><a class="toc-item" href="/books/n/handbook/ch16/#A620">BLAST Output: 2. The Hit Table</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A622"><a class="toc-item" href="/books/n/handbook/ch16/#A622">BLAST Output: 3. Structured Output</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A627"><a class="toc-item" href="/books/n/handbook/ch16/#A627">BLAST Code</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A631"><a class="toc-item" href="/books/n/handbook/ch16/#A631">Appendix 1. FASTA identifiers</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A633"><a class="toc-item" href="/books/n/handbook/ch16/#A633">Appendix 2. Readdb API</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A638"><a class="toc-item" href="/books/n/handbook/ch16/#A638">Appendix 3. Excerpt from a demonstration program doblast.c</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A643"><a class="toc-item" href="/books/n/handbook/ch16/#A643">Appendix 4. A function to print a view of a SeqAlign: MySeqAlignPrint</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A647"><a class="toc-item" href="/books/n/handbook/ch16/#A647">References</a></li></ul></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><div>Kathy Kwan.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch17" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A651"><a class="toc-item" href="/books/n/handbook/ch17/#A651">How Is LinkOut Represented in Entrez?</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A655"><a class="toc-item" href="/books/n/handbook/ch17/#A655">How Does LinkOut Work?</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A668"><a class="toc-item" href="/books/n/handbook/ch17/#A668">Guides for LinkOut Providers</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A677"><a class="toc-item" href="/books/n/handbook/ch17/#A677">Communicating with LinkOut Providers</a></li></ul></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><div>Kim Pruitt, Garth Brown, Tatiana Tatusova, and Donna Maglott.</div><div class="small">Created: October 9, 2002; Last Update: April 6, 2012.</div><ul id="toc_lst_NBK21101_toc_ch18" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch18_Summary"><a class="toc-item" href="/books/n/handbook/ch18/#ch18.Summary">Summary</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch18_Introduction"><a class="toc-item" href="/books/n/handbook/ch18/#ch18.Introduction">Introduction</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch18_Database_Content_Background"><a class="toc-item" href="/books/n/handbook/ch18/#ch18.Database_Content_Background">Database Content: Background</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch18_Assembling_and_Maintaining_the_RefS"><a class="toc-item" href="/books/n/handbook/ch18/#ch18.Assembling_and_Maintaining_the_RefS">Assembling and Maintaining the RefSeq Collection</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch18_Access_and_Retrieval"><a class="toc-item" href="/books/n/handbook/ch18/#ch18.Access_and_Retrieval">Access and Retrieval</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch18_Related_Resources"><a class="toc-item" href="/books/n/handbook/ch18/#ch18.Related_Resources">Related Resources</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch18_Related_Reading"><a class="toc-item" href="/books/n/handbook/ch18/#ch18.Related_Reading">Related Reading</a></li></ul></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><div>Donna Maglott, Kim Pruitt, and Tatiana Tatusova.</div><div class="small">Created: March 3, 2005; Last Update: December 12, 2011.</div><ul id="toc_lst_NBK21101_toc_ch19" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch19_Summary"><a class="toc-item" href="/books/n/handbook/ch19/#ch19.Summary">Summary</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch19_Overview_1"><a class="toc-item" href="/books/n/handbook/ch19/#ch19.Overview_1">Overview</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch19_Maintaining_the_Data"><a class="toc-item" href="/books/n/handbook/ch19/#ch19.Maintaining_the_Data">Maintaining the Data</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch19_How_to_Query_Gene"><a class="toc-item" href="/books/n/handbook/ch19/#ch19.How_to_Query_Gene">How to Query Gene</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch19_Display_Formats"><a class="toc-item" href="/books/n/handbook/ch19/#ch19.Display_Formats">Display Formats</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch19_Content"><a class="toc-item" href="/books/n/handbook/ch19/#ch19.Content">Content</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_ch19_References"><a class="toc-item" href="/books/n/handbook/ch19/#ch19.References">References</a></li></ul></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><div>Susan M. Dombrowski and Donna Maglott.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch20" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1677"><a class="toc-item" href="/books/n/handbook/ch20/#A1677">Introduction</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1563"><a class="toc-item" href="/books/n/handbook/ch20/#A1563">Maintenance of Data</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1573"><a class="toc-item" href="/books/n/handbook/ch20/#A1573">Methods of Access</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1583"><a class="toc-item" href="/books/n/handbook/ch20/#A1583">Interpreting the Display</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1595"><a class="toc-item" href="/books/n/handbook/ch20/#A1595">Customizing the Display</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1612"><a class="toc-item" href="/books/n/handbook/ch20/#A1612">Associated Tools</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1613"><a class="toc-item" href="/books/n/handbook/ch20/#A1613">Technical Details</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1618"><a class="toc-item" href="/books/n/handbook/ch20/#A1618">Caveats for Using Evolving Data</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1624"><a class="toc-item" href="/books/n/handbook/ch20/#A1624">References</a></li></ul></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><div>Joan U. Pontius, Lukas Wagner, and Gregory D. Schuler.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch21" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A858"><a class="toc-item" href="/books/n/handbook/ch21/#A858">Expressed Sequence Tags (ESTs)</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A860"><a class="toc-item" href="/books/n/handbook/ch21/#A860">Sequence Clusters</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A862"><a class="toc-item" href="/books/n/handbook/ch21/#A862">UniGene Cluster Browser</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A863"><a class="toc-item" href="/books/n/handbook/ch21/#A863">Protein Similarity Analysis</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A865"><a class="toc-item" href="/books/n/handbook/ch21/#A865">Digital Differential Display (DDD)</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A866"><a class="toc-item" href="/books/n/handbook/ch21/#A866">HomoloGene</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A868"><a class="toc-item" href="/books/n/handbook/ch21/#A868">References</a></li></ul></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><div>Eugene V. Koonin.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch22" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A886"><a class="toc-item" href="/books/n/handbook/ch22/#A886">Introduction</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A887"><a class="toc-item" href="/books/n/handbook/ch22/#A887">Construction of the COGs</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A897"><a class="toc-item" href="/books/n/handbook/ch22/#A897">Phyletic Pattern Analysis in COGs</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A898"><a class="toc-item" href="/books/n/handbook/ch22/#A898">Description of the COGs Website</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A899"><a class="toc-item" href="/books/n/handbook/ch22/#A899">Future Directions</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A900"><a class="toc-item" href="/books/n/handbook/ch22/#A900">The COG Team</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A901"><a class="toc-item" href="/books/n/handbook/ch22/#A901">References</a></li></ul></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><div>David Wheeler and Barbara Rapp.</div><div class="small">Created: October 9, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch23" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A915"><a class="toc-item" href="/books/n/handbook/ch23/#A915">The User Services Team</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A917"><a class="toc-item" href="/books/n/handbook/ch23/#A917">Development of User Support Materials</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A922"><a class="toc-item" href="/books/n/handbook/ch23/#A922">Outreach</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A935"><a class="toc-item" href="/books/n/handbook/ch23/#A935">Conclusion</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A936"><a class="toc-item" href="/books/n/handbook/ch23/#A936">References</a></li></ul></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><div>David Wheeler, Kim Pruitt, Donna Maglott, Susan Dombrowski, and Andrei Gabrelian.</div><div class="small">Created: November 4, 2002; Last Update: August 13, 2003.</div><ul id="toc_lst_NBK21101_toc_ch24" class="simple-list toc bktoc_lst_exp"><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1680"><a class="toc-item" href="/books/n/handbook/ch24/#A1680">1. How Do I Obtain the Genomic Sequence around My Gene of Interest?</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1684"><a class="toc-item" href="/books/n/handbook/ch24/#A1684">2. If I Have Physical and/or Genetic Mapping Data, How Do I Use the Map Viewer to Find a Candidate Disease Gene in That Region?</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1690"><a class="toc-item" href="/books/n/handbook/ch24/#A1690">3. How Can I Find and Display a Gene with the Map Viewer?</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1697"><a class="toc-item" href="/books/n/handbook/ch24/#A1697">4. How Can I Analyze a Gene Using the Map Viewer?</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1705"><a class="toc-item" href="/books/n/handbook/ch24/#A1705">5. How Can I Create My Own Transcript Models with the Map Viewer?</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1707"><a class="toc-item" href="/books/n/handbook/ch24/#A1707">6. Using the Mouse Map Viewer</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1713"><a class="toc-item" href="/books/n/handbook/ch24/#A1713">7. How Can I Find Members of a Gene Family Using the Map Viewer?</a></li><li class="half_rhythm" id="toc_itm_NBK21101_toc_A1718"><a class="toc-item" href="/books/n/handbook/ch24/#A1718">8. How Can I Find Genes Encoding a Protein Domain Using the Map Viewer?</a></li></ul></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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