697 lines
41 KiB
HTML
697 lines
41 KiB
HTML
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd">
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<html xmlns="http://www.w3.org/1999/xhtml" xml:lang="en" lang="en">
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<head><meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
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<!-- AppResources meta begin -->
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<meta name="paf-app-resources" content="" />
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<!-- Page meta begin -->
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<!-- Page meta end -->
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<!-- Logger begin -->
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<meta xmlns:ncbi-portal="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" name="ncbi_app" content="sviewerdocs" /><meta xmlns:ncbi-portal="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" name="ncbi_pdid" content="sviewerdocs" />
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<title>Searching within the Sequence Viewer</title>
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<meta name="cms-local-nav-url" content="https://cms.ncbi.nlm.nih.gov//sequence-viewer/_nav" />
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<script type="text/javascript" src="/core/jig/1.15.6/js/jig.min.js"></script>
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<!-- AppResources external_resources end -->
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<!-- Page headcontent begin -->
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<meta name="subsite" content="sequence-viewer" />
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<meta name="path" content="sequence-viewer/search" />
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<meta name="modified" content="2021-10-07T00:00:39Z" />
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<link type="text/css" rel="stylesheet" href="/core/assets/gbench/css/gbench-docs.css" /><meta xmlns:ncbi-portal="http://ncbi.gov/portal/XSLT/namespace" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" name="cms-edit-aux-url" content="http://cms.ncbi.nlm.nih.gov/node//edit" />
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<!-- Page headcontent end -->
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<!-- PageFixtures resources end -->
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<link rel="shortcut icon" href="//www.ncbi.nlm.nih.gov/favicon.ico" /><meta name="ncbi_phid" content="CE8B57EF7C8B9A9100000000010400D4.m_5" /><script type="text/javascript"><!--
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var ScriptPath = '/portal/';
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--></script>
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<meta name='referrer' content='origin-when-cross-origin'/><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4201177/css/4121862/3974050/3917732/251717/4092826/3428953/14534/45193/3534283/4128070/3894326/4005757/2867781/3621797.css" /><link type="text/css" rel="stylesheet" href="//static.pubmed.gov/portal/portal3rc.fcgi/4201177/css/3529741/3529739.css" media="print" /><script type="text/javascript">
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var ObjectLinks=[{i:0, ename: "p$ExL", esid:"*", sname: "p$ExL", ssid:"*", dname:"p$el", dsid:"0",m:"CopyValue",p:[],f: function(src, dst) {fn_CopyValue(src, dst);}}]
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var ActiveNames = {"p$ExL":1};
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</script></head>
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<body class=" col2 sviewerdocs">
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<div class="grid">
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<div class="col twelve_col nomargin shadow">
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<!-- System messages like service outage or JS required; this is handled by the TemplateResources portlet -->
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<div class="sysmessages">
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<noscript>
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<p class="nojs">
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<strong>Warning:</strong>
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The NCBI web site requires JavaScript to function.
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<a href="/guide/browsers/#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a>
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</p>
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</noscript>
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</div>
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<!--/.sysmessage-->
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<div class="wrap">
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<div class="page">
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<div xmlns:xi="http://www.w3.org/2001/XInclude">
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<div xmlns="http://www.w3.org/1999/xhtml" id="universal_header" xml:base="http://127.0.0.1/sites/static/header_footer">
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<section class="usa-banner">
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<div class="usa-accordion">
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<header class="usa-banner-header">
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<div class="usa-grid usa-banner-inner">
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<img src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/favicons/favicon-57.png" alt="U.S. flag" />
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<p>An official website of the United States government</p>
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<button class="non-usa-accordion-button usa-banner-button" aria-expanded="false" aria-controls="gov-banner-top" type="button">
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<span class="usa-banner-button-text">Here's how you know</span>
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</button>
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</div>
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</header>
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<div class="usa-banner-content usa-grid usa-accordion-content" id="gov-banner-top" aria-hidden="true">
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<div class="usa-banner-guidance-gov usa-width-one-half">
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<img class="usa-banner-icon usa-media_block-img" src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-dot-gov.svg" alt="Dot gov" />
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<div class="usa-media_block-body">
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<p>
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<strong>The .gov means it's official.</strong>
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<br />
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Federal government websites often end in .gov or .mil. Before
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sharing sensitive information, make sure you're on a federal
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government site.
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</p>
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</div>
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</div>
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<div class="usa-banner-guidance-ssl usa-width-one-half">
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<img class="usa-banner-icon usa-media_block-img" src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-https.svg" alt="Https" />
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<div class="usa-media_block-body">
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<p>
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<strong>The site is secure.</strong>
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<br />
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The <strong>https://</strong> ensures that you are connecting to the
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official website and that any information you provide is encrypted
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and transmitted securely.
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</p>
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</div>
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</div>
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</div>
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</div>
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</section>
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<div class="usa-overlay"></div>
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<header class="ncbi-header" role="banner" data-section="Header">
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<div class="usa-grid">
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<div class="usa-width-one-whole">
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<div class="ncbi-header__logo">
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<a href="/" class="logo" aria-label="NCBI Logo" data-ga-action="click_image" data-ga-label="NIH NLM Logo">
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<img src="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/logos/AgencyLogo.svg" alt="NIH NLM Logo" />
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</a>
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</div>
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<div class="ncbi-header__account">
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<a id="account_login" href="https://account.ncbi.nlm.nih.gov" class="usa-button header-button" style="display:none" data-ga-action="open_menu" data-ga-label="account_menu">Log in</a>
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<button id="account_info" class="header-button" style="display:none" aria-controls="account_popup" type="button">
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<span class="fa fa-user" aria-hidden="true">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 24 24" width="20px" height="20px">
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<g style="fill: #fff">
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<ellipse cx="12" cy="8" rx="5" ry="6"></ellipse>
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<path d="M21.8,19.1c-0.9-1.8-2.6-3.3-4.8-4.2c-0.6-0.2-1.3-0.2-1.8,0.1c-1,0.6-2,0.9-3.2,0.9s-2.2-0.3-3.2-0.9 C8.3,14.8,7.6,14.7,7,15c-2.2,0.9-3.9,2.4-4.8,4.2C1.5,20.5,2.6,22,4.1,22h15.8C21.4,22,22.5,20.5,21.8,19.1z"></path>
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</g>
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</svg>
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</span>
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<span class="username desktop-only" aria-hidden="true" id="uname_short"></span>
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<span class="sr-only">Show account info</span>
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</button>
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</div>
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<div class="ncbi-popup-anchor">
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<div class="ncbi-popup account-popup" id="account_popup" aria-hidden="true">
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<div class="ncbi-popup-head">
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<button class="ncbi-close-button" data-ga-action="close_menu" data-ga-label="account_menu" type="button">
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<span class="fa fa-times">
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<svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 48 48" width="24px" height="24px">
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<path d="M38 12.83l-2.83-2.83-11.17 11.17-11.17-11.17-2.83 2.83 11.17 11.17-11.17 11.17 2.83 2.83 11.17-11.17 11.17 11.17 2.83-2.83-11.17-11.17z"></path>
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</svg>
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</span>
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<span class="usa-sr-only">Close</span></button>
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<h4>Account</h4>
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</div>
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<div class="account-user-info">
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Logged in as:<br />
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<b><span class="username" id="uname_long">username</span></b>
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</div>
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<div class="account-links">
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<ul class="usa-unstyled-list">
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<li><a id="account_myncbi" href="/myncbi/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_myncbi">Dashboard</a></li>
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<li><a id="account_pubs" href="/myncbi/collections/bibliography/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_pubs">Publications</a></li>
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<li><a id="account_settings" href="/account/settings/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_settings">Account settings</a></li>
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<li><a id="account_logout" href="/account/signout/" class="set-base-url" data-ga-action="click_menu_item" data-ga-label="account_logout">Log out</a></li>
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</ul>
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</div>
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</div>
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</div>
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</div>
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</div>
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</header>
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<div role="navigation" aria-label="access keys">
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<a id="nws_header_accesskey_0" href="https://www.ncbi.nlm.nih.gov/guide/browsers/#ncbi_accesskeys" class="usa-sr-only" accesskey="0" tabindex="-1">Access keys</a>
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<a id="nws_header_accesskey_1" href="https://www.ncbi.nlm.nih.gov" class="usa-sr-only" accesskey="1" tabindex="-1">NCBI Homepage</a>
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<a id="nws_header_accesskey_2" href="/myncbi/" class="set-base-url usa-sr-only" accesskey="2" tabindex="-1">MyNCBI Homepage</a>
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<a id="nws_header_accesskey_3" href="#maincontent" class="usa-sr-only" accesskey="3" tabindex="-1">Main Content</a>
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<a id="nws_header_accesskey_4" href="#" class="usa-sr-only" accesskey="4" tabindex="-1">Main Navigation</a>
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</div>
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<section data-section="Alerts">
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<div class="ncbi-alerts-placeholder"></div>
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</section>
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</div>
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</div>
|
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<!--/.header-->
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<div class="header">
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<div class="res_logo"><h1 class="res_name"><a href="/tools/sviewer/" title="NCBI Sequence Viewer home">NCBI Sequence Viewer</a></h1><h2 class="res_tagline"></h2></div>
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<form class="search_form" action="/gquery/" method="get">
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<label for="searchbarlite">Search NCBI </label>
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<input class="jig-ncbiclearbutton" type="text" size="40" id="searchbarlite" name="term" />
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<button type="submit" id="search" class="button_search">Search</button>
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<style type="text/css"></style>
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<input type="hidden" name="p$a" id="p$a" /><input type="hidden" name="p$l" id="p$l" value="PAFAppLayout" /><input type="hidden" name="p$st" id="p$st" value="tools" /><input name="SessionId" id="SessionId" value="CE8B5AF87C7FFCB1_0191SID" disabled="disabled" type="hidden" /><input name="Snapshot" id="Snapshot" value="/projects/staticsites/sviewer/sviewerdoc@1.22" disabled="disabled" type="hidden" /></form>
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</div>
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<div class="nav_and_browser">
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<div class="localnav"><ul data-section="nav-panel-top" class="jig-ncbilocalnav">
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<li> <a href="#">Sequence Viewer</a>
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<ul>
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<li><a href="/projects/sviewer/">Sequence Viewer application</a></li>
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</ul>
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</li>
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<li> <a href="#">General</a>
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<ul>
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<li><a href="/tools/sviewer/about/">About</a></li>
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<li><a href="/tools/sviewer/overview/">Getting started</a></li>
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<li><a href="/tools/sviewer/navigation/">Navigating the Sequence Viewer</a></li>
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<li><a href="/tools/sviewer/release-notes/">Release Notes</a></li>
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</ul>
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</li>
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<li> <a href="#">Help</a>
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<ul>
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<li><a href="/tools/sviewer/videos/">How-to Videos</a></li>
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<li><a href="/tools/sviewer/legends/">Graphical View Legend</a></li>
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<li><a href="/tools/sviewer/faq/">NCBI Track Sets FAQ</a></li>
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</ul>
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</li>
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<li> <a href="#">Interface</a>
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<ul>
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<li><a href="/tools/sviewer/configpanel/">Configure Tracks</a></li>
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<li><a href="/tools/sviewer/overviewpanel/">Overview Panel</a></li>
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<li><a href="/tools/sviewer/graphicalpanel/">Graphical Sequence Panel</a></li>
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<li><a href="/tools/sviewer/sequencepanel/">Sequence Text View</a></li>
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<li><a href="/tools/sviewer/tooltips/">Tooltips</a></li>
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</ul>
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</li>
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<li> <a href="#">Tutorials</a>
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<ul>
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<li><a href="/tools/sviewer/extdata/">Adding custom tracks</a></li>
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<li><a href="/tools/sviewer/markers/">Sequence Markers</a></li>
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<li><a href="/tools/sviewer/search/">Searching within the Sequence Viewer</a></li>
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<li><a href="/tools/sviewer/seqtrackdata/">Download Sequence and Track Data</a></li>
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<li><a href="/tools/sviewer/renderpdf/">Download PDF or SVG images</a></li>
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<li><a href="/tools/sviewer/mrnaproteindata/">Accessing RNA and protein sequence data</a></li>
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<li><a href="/tools/sviewer/translationdiscrepancies/">Displaying translation discrepancies</a></li>
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<li><a href="/tools/sviewer/manual-api/">Using Sequence Viewer Embedding API</a></li>
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</ul>
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</li>
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<li> <a href="#">Manuals</a>
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<ul>
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<li><a href="/tools/sviewer/embedding-api/">NCBI Sequence viewer embedding API</a></li>
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<li><a href="/tools/sviewer/url_access/">URL Parameters</a></li>
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</ul>
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</li>
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<li> <a href="#">Related Resources</a>
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|
<ul>
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|
<li><a href="/projects/treeview/">NCBI Tree Viewer</a></li>
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|
<li><a href="/projects/msaviewer/">NCBI Multiple Sequence Alignment Viewer</a></li>
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</ul>
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<li> <a href="#">Demo pages</a>
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<ul>
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<li><a target="_blank" href="/projects/sviewer/embedded.html">Embedding the NCBI Sequence View in Web Content</a></li>
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<li><a target="_blank" href="/projects/sviewer/MarkerDemo.html">Markers</a></li>
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<li><a target="_blank" href="/projects/sviewer/HGVSDemo.html">HGVS</a></li>
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<li><a target="_blank" href="/projects/sviewer/graphDemo.html">Graph overlay</a></li>
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<li><a target="_blank" href="/projects/sviewer/BAMDemo.html">BAM alignment visualization</a></li>
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<li><a target="_blank" href="/projects/sviewer/event_demo.html">Event listening</a></li>
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</ul>
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</li>
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</li></ul></div>
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</div>
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<!-- was itemctrl -->
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<div class="container">
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<div id="maincontent" class="content col twelve_col last">
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<div class="col1">
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<h1 id="searching-within-the-sequence-vi">Searching within the Sequence Viewer</h1>
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|
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<ul>
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<li><a href="#Coordinate">Sequence Coordinate Searches</a></li>
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<li><a href="#SNP">Search for SNP</a></li>
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<li><a href="#Gene">Search for Gene</a></li>
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<li><a href="#Component">Search for Component</a></li>
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<li><a href="#Sequence">Search Sequence</a></li>
|
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<li><a href="#Track">Track Search</a></li>
|
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</ul>
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|
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|
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<p>When Sequence Viewer is embedded on a web page, or in the stand-alone Sequence Viewer application, searches can be initiated from the “Find:” box on the top toolbar (below, left) or by selecting “Search” in the Tools menu (below, right).</p>
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|
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<p>For information on searching within NCBI genome browsers, such as the Genome Data Viewer (GDV), please see the corresponding <a href="/genome/gdv/browser/help/#SEARCH">Help documentation</a>.</p>
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<p><img src="/core/assets/sequence-viewer/images/Tools_Menu_Search.png" alt="Tools Menu Search" /></p>
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|
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<p>The following terms can be used to search sequence displays:</p>
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|
|
|
|
|
<ul>
|
|
<li>Sequence coordinates</li>
|
|
<li>Reference SNP IDs and HGVS expressions (see <a href="/projects/sviewer/HGVSDemo.html">demo examples</a>)</li>
|
|
<li>Gene symbols</li>
|
|
<li>INSDC nucleotide/protein accessions annotated on the sequence</li>
|
|
<li><a href="/Class/MLACourse/Modules/MolBioReview/iupac_nt_abbreviations.html">IUPAC</a> sequence strings</li>
|
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<li>Keywords found in track names and descriptions</li>
|
|
</ul>
|
|
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|
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<p>Searches are initiated by pressing the Enter key. Successful searches will either update the display or show results in one of the horizontal tabs in the Search Results dialog . </p>
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<p><img src="/core/assets/sequence-viewer/images/Search_Results_Dialog.png" alt="Search Results Dialog" /></p>
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|
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<h2 id="Coordinate">Sequence Coordinate Searches</h2>
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|
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<p>The Sequence Viewer search function can be used to locate a specific position or range. Examples of supported coordinate syntaxes include:</p>
|
|
|
|
|
|
<ul>
|
|
<li>100</li>
|
|
<li>5-515</li>
|
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<li>5..515</li>
|
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<li>5 to 515</li>
|
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<li>10k-20k</li>
|
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<li>1m-2m</li>
|
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</ul>
|
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|
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|
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<p>When a specific coordinate position is entered in the search box, the viewer re-centers at this position at the current zoom level and a <a href="/tools/sviewer/markers/">marker</a> is automatically added at the coordinate. </p>
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<p><img src="/core/assets/sequence-viewer/images/Marker_At_The_Coordinate.png" alt="Marker At The Coordinate" /></p>
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<p>When a coordinate range is entered in the search box, the visible range in the viewer is changed to the specified range. The insets in the image below show that the ends of the visible range correspond to the range in the “Find:” box.</p>
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<p><img src="/core/assets/sequence-viewer/images/Ends_Of_Visible_Range.png" alt="Ends Of Visible Range" /></p>
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|
|
<h2 id="SNP">Search for SNP</h2>
|
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|
|
<p>For human sequences, the Sequence Viewer search function can be used to search for reference SNPs (e.g. rs4970989) from the <a href="/snp/">NCBI SNP database</a>. If the SNP is found in the assembly/molecule, the view moves to the vicinity of the SNP and a <a href="/tools/sviewer/markers/">marker</a> is automatically added at the SNP position.</p>
|
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|
|
<p><img src="/core/assets/sequence-viewer/images/SNP_Search.png" alt="SNP Search" /></p>
|
|
|
|
|
|
<h2 id="Gene">Search for Gene</h2>
|
|
|
|
|
|
<p>You can search for a gene using the gene symbol or full gene name. Results for gene searches appear in the Features tab of the Search Results table. Double-clicking on a search result re-centers the viewer around the gene. </p>
|
|
|
|
|
|
<p><img src="/core/assets/sequence-viewer/images/Gene_Search.png" alt="Gene Search" /></p>
|
|
|
|
|
|
<h2 id="Component">Search for Component</h2>
|
|
|
|
|
|
<p>You can search for contigs or scaffolds that are components of a larger sequence by their accessions. Search results appear in the Components tab of the Search Results table. Double-clicking on a search result re-centers the viewer around the coordinates reported in the table. </p>
|
|
|
|
|
|
<p><img src="/core/assets/sequence-viewer/images/Component_Search.png" alt="Component Search" /></p>
|
|
|
|
|
|
<h2 id="Sequence">Search Sequence</h2>
|
|
|
|
|
|
<p>Sequences can be searched using IUPAC nomenclature for <a href="/Class/MLACourse/Modules/MolBioReview/iupac_nt_abbreviations.html">nucleic acids</a> or <a href="/Class/MLACourse/Modules/MolBioReview/iupac_aa_abbreviations.html">proteins</a>. Regular expressions are supported, e.g. “atg{5}” to find atggggg. Search results appear in the Sequence tab of the Search Results table. Double-clicking on a search result zooms to the sequence match, which is highlighted.</p>
|
|
|
|
|
|
<p><img src="/core/assets/sequence-viewer/images/Sequence_Search.png" alt="Sequence Search" /></p>
|
|
|
|
|
|
<h2 id="Track">Track Search</h2>
|
|
|
|
|
|
<p>The Sequence Viewer search function can also be used to find and add data tracks to the viewer using a keyword in the track name. Only tracks that have been made available to the particular instance of the graphical sequence viewer are in scope for this search. The complete list of available tracks can be found in the <a href="/tools/sviewer/configpanel/">track configuration panel</a>.</p>
|
|
|
|
|
|
<p>Search results appear in the Tracks tab of the Search Results table. A track can be added to the viewer by selecting the check box and clicking the button to “Re-configure”. </p>
|
|
|
|
|
|
<p><img src="/core/assets/sequence-viewer/images/Track_Search.png" alt="Track Search" /></p>
|
|
|
|
|
|
</div>
|
|
<!--/.col1-->
|
|
<div class="col2">
|
|
<div>
|
|
<h2 id="table-of-contents">Table of Contents</h2>
|
|
<ul data-section="TOC-DOC-CLICK">
|
|
<li><a href="/projects/sviewer/">Sequence Viewer application</a></li>
|
|
<li><a href="/tools/sviewer/">Documentation Home</a></li>
|
|
<li>General
|
|
<ul>
|
|
<li><a href="/tools/sviewer/about/">About</a></li>
|
|
<li><a href="/tools/sviewer/overview/">Getting started</a></li>
|
|
<li><a href="/tools/sviewer/navigation/">Navigating the Sequence Viewer</a></li>
|
|
<li><a href="/tools/sviewer/release-notes/">Release Notes</a></li>
|
|
</ul>
|
|
</li>
|
|
<li>Help
|
|
<ul>
|
|
<li><a href="/tools/sviewer/videos/">How-to Videos</a></li>
|
|
<li><a href="/tools/sviewer/legends/">Graphical View Legend</a></li>
|
|
<li><a href="/tools/sviewer/faq/">NCBI Track Sets FAQ</a></li>
|
|
</ul>
|
|
</li>
|
|
<li>Interface
|
|
<ul>
|
|
<li><a href="/tools/sviewer/configpanel/">Configure Tracks</a></li>
|
|
<li><a href="/tools/sviewer/overviewpanel/">Overview Panel</a></li>
|
|
<li><a href="/tools/sviewer/graphicalpanel/">Graphical Sequence Panel</a></li>
|
|
<li><a href="/tools/sviewer/sequencepanel/">Sequence Text View</a></li>
|
|
<li><a href="/tools/sviewer/tooltips/">Tooltips</a></li>
|
|
</ul>
|
|
</li>
|
|
<li>Tutorials
|
|
<ul>
|
|
<li><a href="/tools/sviewer/extdata/">Adding custom tracks</a></li>
|
|
<li><a href="/tools/sviewer/markers/">Sequence Markers</a></li>
|
|
<li><a href="/tools/sviewer/search/">Searching within the Sequence Viewer</a></li>
|
|
|
|
|
|
<li><a href="/tools/sviewer/seqtrackdata/">Download Sequence and Track Data</a></li>
|
|
<li><a href="/tools/sviewer/renderpdf/">Download PDF or SVG images</a></li>
|
|
<li><a href="/tools/sviewer/mrnaproteindata/">Accessing RNA and protein sequence data</a></li>
|
|
<li><a href="/tools/sviewer/translationdiscrepancies/">Displaying translation discrepancies</a></li>
|
|
<li><a href="/tools/sviewer/manual-api/">Using Sequence Viewer Embedding API</a></li>
|
|
</ul>
|
|
</li>
|
|
<li>Manuals
|
|
<ul>
|
|
<li><a href="/tools/sviewer/embedding-api/">Sequence viewer embedding API</a></li>
|
|
<li><a href="/tools/sviewer/url_access/">URL Parameters</a></li>
|
|
</ul>
|
|
</li>
|
|
<li>Demo pages
|
|
<ul>
|
|
<li><a href="/projects/sviewer/embedded.html">Embedding the NCBI Sequence View in Web
|
|
Content</a></li>
|
|
<li><a href="/projects/sviewer/MarkerDemo.html">Markers</a></li>
|
|
<li><a href="/projects/sviewer/HGVSDemo.html">HGVS</a></li>
|
|
<li><a href="/projects/sviewer/graphDemo.html">Graph overlay</a></li>
|
|
<li><a href="/projects/sviewer/BAMDemo.html">BAM alignment visualization</a></li>
|
|
<li><a href="/projects/sviewer/event_demo.html">Event listening</a></li>
|
|
</ul>
|
|
</li>
|
|
<li>Related Resources
|
|
<ul>
|
|
<li><a href="/projects/treeview/">NCBI Tree Viewer</a></li>
|
|
<li><a href="/projects/msaviewer/">NCBI Multiple Sequence Alignment Viewer</a></li>
|
|
</ul>
|
|
</li>
|
|
</ul>
|
|
</div>
|
|
</div>
|
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<!--/.col2-->
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<div class="col3">
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