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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This publication is provided for historical reference only and the information may be out of date.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This publication is provided for historical reference only and the information may be out of date.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 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>
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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><p class="contrib-group">Editors: <span itemprop="editor">Jo McEntyre</span> and <span itemprop="editor">Jim Ostell</span>.</p><a data-jig="ncbitoggler" href="#__NBK21101_ai__" style="border:0;text-decoration:none">Editor Information</a><div style="display:none" class="ui-widget" id="__NBK21101_ai__"><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><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 class="half_rhythm"><ul class="inline_list"><li><span class="label"><a data-jig="ncbidialog" href="#_ncbi_dlg_cpyrght_NBK21101" data-jigconfig="modal:true">Copyright and
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Permissions</a></span></li></ul></div><div id="_ncbi_dlg_cpyrght_NBK21101" style="display:none" title="Copyright and Permissions"><div>This publication is in the public domain. For more information, see the <a href="/books/about/copyright/">Bookshelf Copyright Notice</a>.</div></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 (<a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a>) 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 <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a>, the
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bibliographic database; <a class="def" href="/books/n/handbook/A1237/def-item/app62/">GenBank</a>, the nucleotide sequence database; and the <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a>
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algorithm for sequence comparison, among many others.</p><p>Although each <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> 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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<a class="def" href="/books/n/handbook/A1237/def-item/app59/">gap</a>.</p><p>All of our users know how to execute a straightforward <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> or <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a> 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 <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> 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 <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> 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 <a class="def" href="/books/n/handbook/A1237/def-item/app9/">BLAST</a> 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, <a class="def" href="/books/n/handbook/A1237/def-item/app150/">PubMed</a> query processing
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does not change dramatically year after year.) We hope that The <a class="def" href="/books/n/handbook/A1237/def-item/app116/">NCBI</a> 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><div class="bktoc_all_cntnr top align_right" style="display:none"><ul class="inline_list_right"><li><a class="bktoc_all_exp" href="#">Expand All</a></li><li style="margin-left:.8em"><a class="bktoc_all_clps" href="#">Collapse All</a></li></ul></div><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 class="bktoc_all_cntnr align_right" style="display:none"><ul class="inline_list_right"><li><a class="bktoc_all_exp" href="#">Expand All</a></li><li style="margin-left:.8em"><a class="bktoc_all_clps" href="#">Collapse All</a></li></ul></div></div></div></div>
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