3031 lines
121 KiB
HTML
3031 lines
121 KiB
HTML
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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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<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 -->
|
||
<div class="sysmessages">
|
||
<noscript>
|
||
<p class="nojs">
|
||
<strong>Warning:</strong>
|
||
The NCBI web site requires JavaScript to function.
|
||
<a href="/guide/browsers/#enablejs" title="Learn how to enable JavaScript" target="_blank">more...</a>
|
||
</p>
|
||
</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">
|
||
<header class="usa-banner-header">
|
||
<div class="usa-grid usa-banner-inner">
|
||
<img src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/favicons/favicon-57.png" alt="U.S. flag" />
|
||
<p>An official website of the United States government</p>
|
||
<button class="non-usa-accordion-button usa-banner-button" aria-expanded="false" aria-controls="gov-banner-top" type="button">
|
||
<span class="usa-banner-button-text">Here's how you know</span>
|
||
</button>
|
||
</div>
|
||
</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">
|
||
<p>
|
||
<strong>The .gov means it's official.</strong>
|
||
<br />
|
||
Federal government websites often end in .gov or .mil. Before
|
||
sharing sensitive information, make sure you're on a federal
|
||
government site.
|
||
</p>
|
||
</div>
|
||
</div>
|
||
<div class="usa-banner-guidance-ssl usa-width-one-half">
|
||
<img class="usa-banner-icon usa-media_block-img" src="https://www.ncbi.nlm.nih.gov/coreutils/uswds/img/icon-https.svg" alt="Https" />
|
||
<div class="usa-media_block-body">
|
||
<p>
|
||
<strong>The site is secure.</strong>
|
||
<br />
|
||
The <strong>https://</strong> ensures that you are connecting to the
|
||
official website and that any information you provide is encrypted
|
||
and transmitted securely.
|
||
</p>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
</section>
|
||
<div class="usa-overlay"></div>
|
||
<header class="ncbi-header" role="banner" data-section="Header">
|
||
|
||
<div class="usa-grid">
|
||
<div class="usa-width-one-whole">
|
||
|
||
<div class="ncbi-header__logo">
|
||
<a href="/" class="logo" aria-label="NCBI Logo" data-ga-action="click_image" data-ga-label="NIH NLM Logo">
|
||
<img src="https://www.ncbi.nlm.nih.gov/coreutils/nwds/img/logos/AgencyLogo.svg" alt="NIH NLM Logo" />
|
||
</a>
|
||
</div>
|
||
|
||
<div class="ncbi-header__account">
|
||
<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>
|
||
<button id="account_info" class="header-button" style="display:none" aria-controls="account_popup" type="button">
|
||
<span class="fa fa-user" aria-hidden="true">
|
||
<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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</svg>
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||
</span>
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||
<span class="username desktop-only" aria-hidden="true" id="uname_short"></span>
|
||
<span class="sr-only">Show account info</span>
|
||
</button>
|
||
</div>
|
||
|
||
<div class="ncbi-popup-anchor">
|
||
<div class="ncbi-popup account-popup" id="account_popup" aria-hidden="true">
|
||
<div class="ncbi-popup-head">
|
||
<button class="ncbi-close-button" data-ga-action="close_menu" data-ga-label="account_menu" type="button">
|
||
<span class="fa fa-times">
|
||
<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>
|
||
</svg>
|
||
</span>
|
||
<span class="usa-sr-only">Close</span></button>
|
||
<h4>Account</h4>
|
||
</div>
|
||
<div class="account-user-info">
|
||
Logged in as:<br />
|
||
<b><span class="username" id="uname_long">username</span></b>
|
||
</div>
|
||
<div class="account-links">
|
||
<ul class="usa-unstyled-list">
|
||
<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>
|
||
<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>
|
||
<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>
|
||
<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>
|
||
</ul>
|
||
</div>
|
||
</div>
|
||
</div>
|
||
|
||
</div>
|
||
</div>
|
||
</header>
|
||
<div role="navigation" aria-label="access keys">
|
||
<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>
|
||
<a id="nws_header_accesskey_1" href="https://www.ncbi.nlm.nih.gov" class="usa-sr-only" accesskey="1" tabindex="-1">NCBI Homepage</a>
|
||
<a id="nws_header_accesskey_2" href="/myncbi/" class="set-base-url usa-sr-only" accesskey="2" tabindex="-1">MyNCBI Homepage</a>
|
||
<a id="nws_header_accesskey_3" href="#maincontent" class="usa-sr-only" accesskey="3" tabindex="-1">Main Content</a>
|
||
<a id="nws_header_accesskey_4" href="#" class="usa-sr-only" accesskey="4" tabindex="-1">Main Navigation</a>
|
||
</div>
|
||
<section data-section="Alerts">
|
||
<div class="ncbi-alerts-placeholder"></div>
|
||
</section>
|
||
</div>
|
||
</div>
|
||
<!--/.header-->
|
||
<div class="header">
|
||
<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>
|
||
|
||
<form class="search_form" action="/gquery/" method="get">
|
||
<label for="searchbarlite">Search NCBI </label>
|
||
<input class="jig-ncbiclearbutton" type="text" size="40" id="searchbarlite" name="term" />
|
||
<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>
|
||
|
||
|
||
</div>
|
||
<div class="nav_and_browser">
|
||
<div class="localnav"><ul data-section="nav-panel-top" class="jig-ncbilocalnav">
|
||
<li> <a href="#">Sequence Viewer</a>
|
||
<ul>
|
||
<li><a href="/projects/sviewer/">Sequence Viewer application</a></li>
|
||
</ul>
|
||
</li>
|
||
<li> <a href="#">General</a>
|
||
<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> <a href="#">Help</a>
|
||
<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> <a href="#">Interface</a>
|
||
<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> <a href="#">Tutorials</a>
|
||
<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> <a href="#">Manuals</a>
|
||
<ul>
|
||
<li><a href="/tools/sviewer/embedding-api/">NCBI Sequence viewer embedding API</a></li>
|
||
<li><a href="/tools/sviewer/url_access/">URL Parameters</a></li>
|
||
</ul>
|
||
</li>
|
||
<li> <a href="#">Related Resources</a>
|
||
<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> <a href="#">Demo pages</a>
|
||
<ul>
|
||
<li><a target="_blank" href="/projects/sviewer/embedded.html">Embedding the NCBI Sequence View in Web Content</a></li>
|
||
<li><a target="_blank" href="/projects/sviewer/MarkerDemo.html">Markers</a></li>
|
||
<li><a target="_blank" href="/projects/sviewer/HGVSDemo.html">HGVS</a></li>
|
||
<li><a target="_blank" href="/projects/sviewer/graphDemo.html">Graph overlay</a></li>
|
||
<li><a target="_blank" href="/projects/sviewer/BAMDemo.html">BAM alignment visualization</a></li>
|
||
<li><a target="_blank" href="/projects/sviewer/event_demo.html">Event listening</a></li>
|
||
</ul>
|
||
</li>
|
||
</li></ul></div>
|
||
</div>
|
||
|
||
<!-- was itemctrl -->
|
||
<div class="container">
|
||
<div id="maincontent" class="content col twelve_col last">
|
||
<div class="col1">
|
||
<h1 id="ncbi-graphical-sequence-viewer-e"><strong>NCBI Graphical Sequence Viewer Embedding API</strong></h1>
|
||
|
||
|
||
<h2 id="sequence-viewer-revision-330-and">Sequence Viewer Revision: 3.30 and newer</h2>
|
||
|
||
|
||
<h2 id="contents">Contents</h2>
|
||
|
||
|
||
<ul>
|
||
<li><a href="#bookmark0">Introduction</a></li>
|
||
<li><a href="#bookmark1">Including Sequence Viewer on a web page</a></li>
|
||
<li><a href="#bookmark2">Including Sequence Viewer in an iFrame</a><ul>
|
||
<li><a href="#iframecode">How to obtain code of the Sequence Viewer for embedding</a></li>
|
||
<li><a href="#bookmark3">How to include Sequence Viewer on a web page in an <iframe></a> </li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#bookmark4">Sequence Viewer parameters</a><ul>
|
||
<li><a href="#bookmark5">Base parameters</a></li>
|
||
<li><a href="#bookmark6">Advanced parameters</a></li>
|
||
<li><a href="#bookmark7">Events sent by SV instance</a></li>
|
||
<li><a href="#bookmark8">Examples</a></li>
|
||
<li><a href="#bookmark9">Example web pages</a></li>
|
||
<li><a href="#bookmark10">Cross-domain embedding</a></li>
|
||
<li><a href="#bookmark10A">Web tracks upload/embedding</a></li>
|
||
<li><a href="#bookmark10B">SRA tracks embedding</a></li>
|
||
<li><a href="#bookmark10E">Alignment tracks from AlignDb</a></li>
|
||
<li><a href="#bookmark10C">Remote (HTTP-based) BAM files</a></li>
|
||
<li><a href="#bookmark10d">BigBED and BigWIG files</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#bookmark11">Appendix A: Tracks Parameters</a></li>
|
||
<li><a href="#bookmark12">‘tracks’ parameter syntax</a><ul>
|
||
<li><a href="#bookmark15">key: six_frames_translation</a></li>
|
||
<li><a href="#bookmark16">key:alignment_track</a></li>
|
||
<li><a href="#bookmark17">key:gene_model_track</a></li>
|
||
<li><a href="#bookmark18">key:SNP_track</a></li>
|
||
<li><a href="#bookmark19">key:feature_track</a></li>
|
||
<li><a href="#bookmark19A">key:aggregate_feature_track</a></li>
|
||
<li><a href="#bookmark20">key:dbvar_track</a></li>
|
||
<li><a href="#bookmark20a">key:graph_track</a></li>
|
||
<li><a href="#bookmark20b">key:graph_overlay</a></li>
|
||
<li><a href="#bookmark20c">key:trace_track</a></li>
|
||
<li><a href="#bookmark21">Key:user_data_track</a></li>
|
||
<li><a href="#bookmark22">‘tracks’ parameter examples</a></li>
|
||
</ul>
|
||
</li>
|
||
<li><a href="#bookmark23">Appendix B: Feature Subtype Storage Keys 23</a></li>
|
||
<li><a href="#bookmark24">Appendix C: Objects/Features tooltips preprocessing</a></li>
|
||
</ul>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<h2 id="bookmark0">Introduction</h2>
|
||
|
||
|
||
<p>The NCBI Graphical Sequence Viewer (SV) is a general purpose tool for viewing biological sequence data. It can be embedded in a wide variety of web pages and with a large number of options. This document serves as a launching point to understand how to embed the Sequence Viewer in any context. For purposes of standardization in this document, all links presented include the common refrain <a href="https://www.ncbi.nlm.nih.gov">http://www.ncbi.nlm.nih.gov</a> .</p>
|
||
|
||
|
||
<p>If you have questions or need help, please <a href="https://support.nlm.nih.gov/support/create-case/">contact us</a>.</p>
|
||
|
||
|
||
<p>Additional documentation can be found at <a href="/tools/sviewer/">http://www.ncbi.nlm.nih.gov/tools/sviewer/</a>.</p>
|
||
|
||
|
||
<p>A tutorial with examples is available <a href="/tools/sviewer/manual-api/">here</a> and you can get a list of <a href="/tools/sviewer/url_access/">URL parameters here</a>. </p>
|
||
|
||
|
||
<h2 id="bookmark1">Including Sequence Viewer on a web page</h2>
|
||
|
||
|
||
<p>The Sequence Viewer is implemented using an ExtJS JavaScript library. </p>
|
||
|
||
|
||
<ol>
|
||
<li>
|
||
<p>There is no need to declare or load ExtJS css files or js scripts. SV dynamically loads everything it needs from the www.ncbi.nlm.nih.com website. On the other hand if ExtJS scripts are declared/loaded before sviewer.js declaration, SV omits their loading to allow an embedding application to use a specific edition of the library. The following example demonstrate how to declare SV script:</p>
|
||
<p><script type=”text/javascript” src=”http://www.ncbi.nlm.nih.gov/projects/sviewer/js/sviewer.js”></script></p>
|
||
</li>
|
||
<li>
|
||
<p>If an embedding application does not create SV instances dynamically the following inlining of Sequence Viewer script (includes id="autoload”) allows the SV application to find appropriate SeqViewerApp declarations and create instances automatically (with data loading):</p>
|
||
<p><script type=”text/javascript” src=”http://www.ncbi.nlm.nih.gov/projects/sviewer/js/sviewer.js” id="autoload”></script></p>
|
||
<p>SeqViewerApp must be declared as <div> tag with class='SeqViewerApp' and one <a> tag where href attribute containing SViewer parameters. An example is:</p>
|
||
<p><div id='some-id' class='SeqViewerApp'>
|
||
<a href='?embedded=true&id=…'><a>
|
||
</div></p>
|
||
<p>You do not use this method if the Sequence Viewer div is initially hidden. Use the method from point 3 to instantiate Sequence Viewer dynamically.</p>
|
||
</li>
|
||
<li>
|
||
<p>If an embedding application needs to create SV instances dynamically the following example demonstrates how to declare them and initiate SV instances creation and loading manually (SV script declaration from point 3):</p>
|
||
<p><div id=’sv1’></div>
|
||
...
|
||
<script type='text/javascript'>
|
||
SeqViewOnReady(function()
|
||
{ var app = new SeqView.App(‘sv1’); app.load(‘embedded=true&id=…’); }
|
||
);
|
||
</script></p>
|
||
<p>In this case the application may not use class name (or any) for the div.</p>
|
||
</li>
|
||
<li>
|
||
<p>Function SeqViewOnReady(callback, [scope]) is designed to prevent SV usage before SeqView class is initialized.</p>
|
||
<p>Parameters:</p>
|
||
<p><strong>callback</strong> - user callback function
|
||
<strong>scope</strong> - callback function scope (if necessary)</p>
|
||
</li>
|
||
</ol>
|
||
|
||
|
||
<p>For a video tutorial please watch the following video:</p>
|
||
|
||
|
||
<p><a href="https://www.youtube.com/watch?v=JC10DCKAfyM&feature=youtu.be"><img src="/core/assets/sequence-viewer/images/embed-sv-into-your-pages.png" alt="Embed the NCBI Sequence Viewer into Your Pages" width="400" />
|
||
Embed the NCBI Sequence Viewer into Your Pages</a></p>
|
||
|
||
|
||
<h2 id="bookmark2">Including Sequence Viewer in an iFrame</h2>
|
||
|
||
|
||
<h3 id="iframecode">How to obtain code of the Sequence Viewer for embedding</h3>
|
||
|
||
|
||
<p>The suggested workflow is:</p>
|
||
|
||
|
||
<ol>
|
||
<li>Pick a molecule of interest, which illustrates the case. Use GDV or enter your accession at: <a href="https://www.ncbi.nlm.nih.gov/projects/sviewer/">https://www.ncbi.nlm.nih.gov/projects/sviewer/</a></li>
|
||
<li>Find and zoom to the region of interest (it could be a gene or a specific mutation). </li>
|
||
<li>Add <a href="/tools/sviewer/markers">markers</a> (if desired) to annotate your region.</li>
|
||
<li>Pick tracks of interest using the <a href="/tools/sviewer/configpanel/">track configuration panel</a></li>
|
||
<li>Change track display options if desired.</li>
|
||
<li>Use the “Link to This View” option to show code. </li>
|
||
</ol>
|
||
|
||
|
||
<p><a href="/core/assets/sequence-viewer/images/link_to_this_page_dialog.png"><img src="/core/assets/sequence-viewer/images/link_to_this_page_dialog.png" alt="link to this page dialog" class="sshot" /></a></p>
|
||
|
||
|
||
<p>The resulting code will contain parameters that capture the sequence molecule, location, and track and marker configuration of your view. </p>
|
||
|
||
|
||
<p>There are two types of embedding code. The first option, ‘Embed code for IFRAME’, can be used as is to embed the Sequence Viewer by itself as an IFRAME. The second option,‘Whole page example,’ can be used to embed the Sequence Viewer as a part of your page. This option has both the script in the HEAD element and DIV element with parameters.</p>
|
||
|
||
|
||
<h3 id="bookmark3">How to include Sequence Viewer in a web page in an <iframe></h3>
|
||
|
||
|
||
<p>The NCBI Sequence Viewer can be embedded as an IFRAME. When configured, Sequence Viewer will automatically resize the enclosing iframe vertically to avoid scroll bars.</p>
|
||
|
||
|
||
<p>To use iframe embedding, add this to your page:</p>
|
||
|
||
|
||
<p><iframe id="sviframe" src="/projects/sviewer/embedded_iframe.html?iframe=sviframe&id=nt_011515" width="900"></p>
|
||
|
||
|
||
<p>Please note :</p>
|
||
|
||
|
||
<ol>
|
||
<li>iframe id can be arbitrary, and it should be passed to the source URL as parameter 'iframe' (“sviframe” in the example above)</li>
|
||
<li>iframe content page (“/projects/sviewer/embedded_iframe.html” in the example) should belong to the same domain as the main page (take the page and save it on your server)</li>
|
||
<li>iframe should satisfy the minimal width requirement of 800 pixels to accommodate the pop-up interface elements of the Sequence Viewer</li>
|
||
</ol>
|
||
|
||
|
||
<p>There can be issues using multiple libraries that reset style sheets. If you have any issues with the style sheets used in ExtJS/Sequence Viewer, i.e. Sequence Viewer doesn’t look right, try adding this directive:</p>
|
||
|
||
|
||
<p><link rel="stylesheet" type="text/css" href="http://www.ncbi.nlm.nih.gov/projects/sviewer/css/sv-cleanup.css"></p>
|
||
|
||
|
||
<h2 id="bookmark4">Sequence Viewer parameters</h2>
|
||
|
||
|
||
<p>Parameters may be passed to Sequence Viewer by putting them in the included <a href=''> link tag within the Sequence Viewer <div> tag.</p>
|
||
|
||
|
||
<h3 id="bookmark5">Base parameters:</h3>
|
||
|
||
|
||
<p>The color used for highlighting can be changed per track using the track specific <strong>highlights_color</strong> parameter.</p>
|
||
|
||
|
||
<ol>
|
||
<li><strong>embedded={false, true, minimal, panorama}</strong> – removes some components that are not needed in embedded mode (panorama view, some links) if 'minimal' value is passed then only a bare-bone image is shown with buttons-only tool bar and without panel header. If ‘panorama’ is passed then only the top panel, the Overview panel, is shown.
|
||
Default is false. This is a required parameter for an embedded version of SV.</li>
|
||
<li><strong>id=<string></strong> - GI of a sequence to show. Required parameter.1,2,3</li>
|
||
<li><strong>noviewheader={true,false}</strong> – removes header from a sequence view. This parameter only relevant when embedded=true. Default is false. Optional parameter.</li>
|
||
<li><strong>v=<view ranges></strong> - sets a specified visible range to a graphical panel. If not specified the whole sequence is shown.
|
||
(Example: v=1000:6000,100k:2m, 100K-2M, 100k..2M). Optional parameter.</li>
|
||
<li>
|
||
<p><strong>mk=<position or range>|<marker name>|<color in RGB hex></strong> Use the mk parameter to set a marker at a position or on a range of positions. Multiple markers can be set by separating the each entry with a comma. Use an exclamation point ("!") after an entry to lock the marker. A locked marker is fixed in the graphical view. The name and color parameters are <em>optional</em> .
|
||
Examples:</p>
|
||
<p><strong>mk=1000</strong> puts an unlocked marker with default color and name at position 1000
|
||
<strong>mk=1000:2000</strong> puts an unlocked marker with default color and name on the range 1000-2000
|
||
<strong>mk=1000:2000|TestMarker</strong> puts an unlocked marker with default color and the name "TestMarker" on the range 1000-2000
|
||
<strong>mk=1000:2000|TestMarker|00ff00</strong> puts an unlocked marker with color 0x00ff00 and the name "TestMarker" on the range 1000-2000
|
||
<strong>mk=1000:2000|TestMarker|00ff00,3000:4000|TestMarker2|80ff10</strong> puts an unlocked marker with color 0x00ff00 and the name "TestMarker" on the range 1000-2000 and another unlocked marker with color 0x80ff10 and the name "TestMarker2" on the range 3000-4000.
|
||
<strong>mk=1000:2000|TestMarker|00ff00,3000:4000|TestMarker2|80ff10!</strong> - same as above with a lock on "TestMarker2". Note: Special characters in marker names must be escaped properly usually with a \ prepended.</p>
|
||
</li>
|
||
<li>
|
||
<p><strong>toolbar = <nspztcrhgmd></strong> Specifies which options are present on the toolbar. This parameter is optional and if omitted, all options are shown. If any options are specified, all other options must be opted in.</p>
|
||
<ul>
|
||
<li>n - Name button</li>
|
||
<li>s – Search field</li>
|
||
<li>p - Panning buttons</li>
|
||
<li>z - Zoom slider & buttons</li>
|
||
<li>t - Tools menu</li>
|
||
<li>c - Configure menu</li>
|
||
<li>r - Reload button</li>
|
||
<li>h - Help button</li>
|
||
<li>g - Gene render mode button (switches on "Show All" mode for gene tracks features)</li>
|
||
<li>m - Switch mode (Slim/Normal) button</li>
|
||
<li>d - Download menu</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p><strong>origin=<sequence position></strong> - Set the sequence origin. Optional parameter. (Example: origin=5000)</p>
|
||
</li>
|
||
<li><strong>flip=true</strong> - Flips the strand. Default is false. (Example: flip=true or flip=false) . Optional parameter.</li>
|
||
<li><strong>strand=true</strong> - Synonym for flip parameter. Optional parameter</li>
|
||
<li><strong>assm_context=GC Assembly accession</strong> – Defines the assembly accession used for retrieving track configuration for a given application context from track manager service. Optional parameter. It is required only when using SViewer inside a genome browser that uses track manager service to manager data tracks.</li>
|
||
<li><strong>app_context=Unique and preregistered genome browser application name</strong> – It differs from ‘appname’ below. ‘app_context’ is preregistered in track manager service. A combination of ‘app_context’ and ‘assm_context’ define a set of data tracks to be shown in the given application context. Optional parameter. It is required only when using SViewer inside a genome browser that uses track manager service to manager data tracks.</li>
|
||
<li>
|
||
<p><strong>appname=<string></strong> - Defines the name of the client calling the application. This is an optional parameter used in storing a user’s configuration settings; we recommend that all developers supply an application name. The name chosen should be unique; this name will appear in a cookie set in the user’s browser to indicate storage of configuration information. We strongly recommend that callers avoid using generic phrases like “gene” or “viewer”, and prepend a namespace (i.e., “NcbiPortalGene” or “XYZViewer”). If there are questions about what name to use, please contact the sequence viewer team. (sviewer-service AT ncbi.nlm.nih.gov)
|
||
Example:</p>
|
||
<p><div id="SeqViewer0" class="SeqViewerApp">
|
||
<a href="?id=89161185&embedded=true&appname=testemb&v=1:247249719 &tracks=[key:graph_track,annots:NA0000016.1|]"></a>
|
||
</div></p>
|
||
</li>
|
||
<li>
|
||
<p><strong>multipanel={true, false}</strong> – permits or prohibits the use of multiple graphical panels in one Sequence Viewer instance. If not specified, it is default to 'true' in standalone mode and to 'false' in embedded mode.</p>
|
||
</li>
|
||
<li><strong>slim=<true></strong> - Constitutes the set of initial modes for graphical panels. Slim Mode displays tracks without title bars. Default is false. This is an optional parameter. (Example:slim=true, false, true or slim=1,0,1)</li>
|
||
<li>a. <strong>nopdf=</strong> <strong>{true, false}</strong> - Disables PDF printing option. Default is false. (Example: nopdf=true or nopdf=false). This is an optional parameter. <br />
|
||
b. <strong>notrdata=true</strong> - Removes option Download Track Data from Download menu. Default is false.</li>
|
||
<li><strong>nosavetracks</strong> - Disables menu item "Save current tracks" in "My NCBI Track Collections" menu.</li>
|
||
<li>
|
||
<p><strong>highlights_color=<html-format color=""></html-format></strong> is optional. When specified, it defines the color to be used for highlights in all tracks. Accepted formats:</p>
|
||
<ul>
|
||
<li>A named color, such as "red", "blue", "salmon", etc. Supports <a href="http://www.w3schools.com/colors/colors_names.asp">HTML color names</a></li>
|
||
<li>HTML-format colors, such as "#f0f0dd", or "f0f0dd". These are accepted with or without the leading '#'.
|
||
The color used for highlighting can also be changed per track using the track specific <strong>highlights_color</strong> parameter.</li>
|
||
</ul>
|
||
<p>Sample URL parameters: id=NC_000005.10&minheight=220&client=seqviewer&width=3999&view_width=970&from=68710561&len=1485030&assm_context=
|
||
GCF_000001405.33&label=Default&color=Color&decor=Default&spacing=Normal&content=Details&tracks=[key:gene_model_track,name:Genes,display_name:Track1,id:STD14,category:Genes,annots:Unnamed,Options:
|
||
MergeAll,SNPs:false,CDSProductFeats:false,highlights:GeneID\:5884, <span style="color:#f00;"> <strong>highlights_color:red</strong> </span> ,
|
||
ShowLabelsForAllFeatures:false,NtRuler:true,AaRuler:false]key:gene_model_track,name:T577824,display_name:
|
||
Track2,id:T577824,category:Genes,subcategory:NCBI,dbname:SADB,annots:NA000077605.1,highlights:
|
||
GeneID\:100506658,Options:MergeAll,SNPs:false,CDSProductFeats:false,ShowLabelsForAllFeatures:false,
|
||
NtRuler:true,AaRuler:false]& <span style="color:#00f;"> <strong>highlights_color=blue</strong> </span>
|
||
In the sample above the global <strong>highlights_color</strong> parameter changes the highlighting color for all tracks to blue, the track specific highlights_color parameter overrides the color for the first track to red:</p>
|
||
<p><img src="/core/assets/sequence-viewer/images/highlights-color-sample.png" alt="highlights color sample" /></p>
|
||
</li>
|
||
</ol>
|
||
|
||
|
||
<h3 id="bookmark6">Advanced parameters:</h3>
|
||
|
||
|
||
<ol>
|
||
<li><strong>rid=<rid></strong> - Option to load BLAST results stored as an RID. Optional parameter .4,5</li>
|
||
<li><strong>tracks=[<track1_descr>,<track2_descr>]</strong> - Specify tracks that should be rendered. Optional parameter. See Appendix A for examples.</li>
|
||
</ol>
|
||
|
||
|
||
<h3 id="bookmark7">Events sent by SV instance:</h3>
|
||
|
||
|
||
<p>An application that uses SV can subscribe to events that SV will send in case of a user interaction with SV. Here is the list of supported events:</p>
|
||
|
||
|
||
<p><strong>'panorama_image_loaded'</strong> - fired when panorama image is loaded to application '
|
||
<strong>'graphical_image_loaded'</strong> - fired when graphical image is loaded to view 'marker_created' - fired when marker is created in view
|
||
<strong>'marker_deleted'</strong> - fired when marker is deleted in view
|
||
<strong>'feature_clicked'</strong> - fired when feature is clicked in view
|
||
<strong>'origin_changed'</strong> - fired when origin is changed for application
|
||
<strong>'strand_changed'</strong> - fired when strand is changed
|
||
<strong>'visible_range_changed'</strong> - fired when visible range is changed (for example, zoom or shift)
|
||
<strong>'configuration_changed'</strong> - fired when configuration is changed (for example, tracks are added)</p>
|
||
|
||
|
||
<p>The subscription object for any events is SViewer application (object SeqView.App). Every event has a reference to its source provided. Events related to particular view are provided with view object, others are provided with application object. Here is an example of use:</p>
|
||
|
||
|
||
<p>function initSviewerApp(sviewer){ sviewer.on({ 'visible_range_changed': function(view) { // event processing }, 'graphical_image_loaded': function(view) { // event processing }); }</p>
|
||
|
||
|
||
<p>Also SViewer application provides some number of access functions.</p>
|
||
|
||
|
||
<p><strong>getApps()</strong> - returns the list of all applications on the current HTML page
|
||
<strong>getTracks()</strong> - provides loaded tracks for particular application
|
||
<strong>getConfiguration()</strong> - provides the configuration object for particular application</p>
|
||
|
||
|
||
<p>Example:</p>
|
||
|
||
|
||
<p>var app = SeqView.App.findAppByDivId(‘YOUR_SV_DIV_ID’);
|
||
app.on({
|
||
visible_range_changed: function(view) {
|
||
console.log(view.m_VisFromSeq + ' - ' + view.m_VisLenSeq);
|
||
},
|
||
marker_created: function(marker) { … },
|
||
marker_deleted: function(marker) { … },
|
||
graphical_image_loaded: function(view) { … },
|
||
feature_clicked: function(view, feat) { … },
|
||
scope: this
|
||
});</p>
|
||
|
||
|
||
<h3 id="bookmark8">Examples:</h3>
|
||
|
||
|
||
<p><div style="padding:10px;">
|
||
<div id="sv1" class="SeqViewerApp" >
|
||
<a href="?embedded=true&id=NC_003284&from=13598210&to=13599776"> </a>
|
||
</div>
|
||
</div></p>
|
||
|
||
|
||
<p><img src="/core/assets/sequence-viewer/images/Image_005.jpg" alt="Example1" /></p>
|
||
|
||
|
||
<p><div style="padding:10px;">
|
||
<div id="sv1" class="SeqViewerApp" >
|
||
<a href= "?embedded=minimal&id=NC_003284&from=13598210&to=13599776&mk=13598700:13598925|Marker1|008000"></a>
|
||
</div>
|
||
</div></p>
|
||
|
||
|
||
<p><img src="/core/assets/sequence-viewer/images/Image_006.jpg" alt="Example2" /></p>
|
||
|
||
|
||
<h3 id="bookmark9">Example web pages:</h3>
|
||
|
||
|
||
<ol>
|
||
<li>Embedding Sequence Viewer into a standalone web page.
|
||
<a href="/projects/sviewer/embedded.html">http://www.ncbi.nlm.nih.gov/projects/sviewer/embedded.html</a></li>
|
||
<li>Embedding Sequence Viewer and collecting its events. The example includes controlled SeqView.App launch (via SeqViewOnReady function):
|
||
<a href="/projects/sviewer/event_demo.html">http://www.ncbi.nlm.nih.gov/projects/sviewer/event_demo.html</a></li>
|
||
</ol>
|
||
|
||
|
||
<h3 id="bookmark10">Cross-domain embedding</h3>
|
||
|
||
|
||
<p>Previously we recommended to set up redirecting scripts on the embedder's site. Now, as we support Internet standard CORS it is no longer needed.</p>
|
||
|
||
|
||
<h3 id="bookmark10A">Web tracks upload/embedding</h3>
|
||
|
||
|
||
<p>There is a new ability allowing to add multiple user data items and assign them names through parameters to Sequence Viewer.</p>
|
||
|
||
|
||
<p>Before this only one item of each type (URL, Blast RID, or inline ASN.1 text) could be used, and track names were assigned automatically based on the data itself.</p>
|
||
|
||
|
||
<p>New parameter, 'tn' (short for Track Name) is introduced for this purpose. This parameter can be present several times and corresponds to the data item (url, rid, or data parameter) in the order of occurrence. E.g., if you have an RID and data file and would like to display them and assign these track names, the following syntax should be used:</p>
|
||
|
||
|
||
<p><a href="/projects/sviewer/?id=NC_000001.10&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.short.bed&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.bed&tn=Some%20USCS%20genes&tn=Some%20other%20genes&v=660932:2480277">http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_000001.10&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.short.bed&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.bed&tn=Some%20USCS%20genes&tn=Some%20other%20genes&v=660932:2480277</a></p>
|
||
|
||
|
||
<p>The same syntax works for embedding Sequence Viewer in your own pages:</p>
|
||
|
||
|
||
<p><div id="some-id" <class="SeqViewerApp">
|
||
<a href="?embedded=true&id=NC_000001.10&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.short.bed&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.bed&tn=Some%20USCS%20genes&tn=Some%20other%20genes&v=660932:2480277"></a>
|
||
</div></p>
|
||
|
||
|
||
<p>The files used for 'url' parameter should be accessible through public HTTP or FTP.</p>
|
||
|
||
|
||
<p>If you'd like to name only the second data item, you ought to include empty track name parameter for the first item:</p>
|
||
|
||
|
||
<p><a href="https://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_000001.10&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.short.bed&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.bed&tn=&tn=Some%20other%20genes&v=660932:2480277">http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_000001.10&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.short.bed&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.bed&tn=&tn=Some%20other%20genes&v=660932:2480277</a></p>
|
||
|
||
|
||
<p>Same thing can be done with other data types, such as Blast RID:</p>
|
||
|
||
|
||
<p><a href="https://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_000001.10&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.bed&rid=G9TDMFBP016&tn=Some%20external%20genes&tn=Some%20alignments&v=1570103:1594554">http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_000001.10&url=https://ftp.ncbi.nlm.nih.gov/toolbox/gbench/samples/UCSCGenes_exon20.bed&rid=G9TDMFBP016&tn=Some%20external%20genes&tn=Some%20alignments&v=1570103:1594554</a></p>
|
||
|
||
|
||
<p>Unfortunately, the Blast RID is valid for only a short time. To obtain a more permanent view for your data, we recommend exporting the data as an alignment file (ASN or BAM). </p>
|
||
|
||
|
||
<p>Sequence Viewer now supports two parameters with the same syntax but different behavior:
|
||
<strong>url</strong> and <strong>url_reload</strong></p>
|
||
|
||
|
||
<p>Parameter <strong>url</strong> uploads the target file once and uses it for visualization. If underlying data changes you have to change the file name as well, otherwise Sequence Viewer will keep showing the old data (until some potentially long timeout period expires). You file name naming scheme may need some versioning.</p>
|
||
|
||
|
||
<p>Parameter <strong>url_reload</strong> always tries to re-upload the file to check the content, which can introduce a processing delay. If you use this parameter you don't have to create a file name versioning but this mode will be slower as it needs to download the file every time.</p>
|
||
|
||
|
||
<h3 id="bookmark10B">SRA tracks embedding</h3>
|
||
|
||
|
||
<p>An SRA track can be referenced in three different ways, by either using an SRR accession (e.g. SRR505885), or a NCBI Internal file path (e.g. /netmnt/traces04/sra2/SRR/001282/SRR1313308), or a URL (e.g. <a href="https://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR131/SRR1313308/SRR1313308.sra">http://ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR131/SRR1313308/SRR1313308.sra</a>).</p>
|
||
|
||
|
||
<p>The Sequence viewer accepts a comma-delimited list of SRR accessions in a srz parameter. A comma-delimited list of file paths and/or URLs is accepted in bam_path parameter (despite its name, this parameter accepts both BAM and SRA formatted files).</p>
|
||
|
||
|
||
<p>For defining SRA tracks via the "tracks" parameter, two of its settings are used: "dbname" and "annots". "dbname" must be set to "SRA" if an SRR accession is going to be used and to "cSRA" for file paths or URLs (SRA or BAM formatted). "annots" holds a SRR accession or file path/URL (please note that all colons including the one in "http://" prefix must be escaped with a backslash).</p>
|
||
|
||
|
||
<p><strong>srz</strong> - sets the SRR (SR Run) to use as a datasource for a track, expands to proper track description, e.g. srz=ERR276220 expands into tracks=[key:alignment_track,name:ERR276220,display_name:ERR276220,dbname:SRA,category:Alignments,setting_group:cSRA,annots:ERR276220]</p>
|
||
|
||
|
||
<p><strong>bam_path</strong> - BAM file's url or path (NCBI Internal) to BAM file</p>
|
||
|
||
|
||
<h4 id="examples">Examples</h4>
|
||
|
||
|
||
<p><a href="/projects/sviewer/?id=AM180355.1&srz=ERR276220">Explicit srz parameter for SRR</a></p>
|
||
|
||
|
||
<p><a href="/projects/sviewer/?id=AM180355.1&tracks=[amend][key:alignment_track,name:ERR276220,display_name:ERR276220,dbname:SRA,category:Alignments,setting_group:cSRA,annots:ERR276220]">Same SRR expressed as track with dbname = SRA</a></p>
|
||
|
||
|
||
<p><a href="/projects/sviewer/?id=NC_000001.11&assm_context=GCF_000001405.35&bam_path=https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/NIST_HiSeq_HG002_Homogeneity-10953946/NHGRI_Illumina300X_AJtrio_novoalign_bams/HG002.GRCh38.300x.bam">Explicit bam_path for external BAM file</a></p>
|
||
|
||
|
||
<p><a href="/projects/sviewer/?id=NC_000001.11&assm_context=GCF_000001405.35&tracks=[amend][key:alignment_track,dbname:cSRA,annots:https\://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG002_NA24385_son/NIST_HiSeq_HG002_Homogeneity-10953946/NHGRI_Illumina300X_AJtrio_novoalign_bams/HG002.GRCh38.300x.bam]">Same BAM file expressed as track with dbname = cSRA</a></p>
|
||
|
||
|
||
<p><a href="/projects/sviewer/seqgraphic.cgi?id=NC_000001.10&minheight=220&client=seqviewer&width=1370&from=0&len=249250621&label=Default&color=Color&decor=Default&spacing=Normal&content=Details&tracks=%5Bkey:alignment_track,name:SRR505885,display_name:SRR505885,id:STD72,category:Alignments,dbname:SRA,annots:SRR505885,Layout:AdaptiveSeq,StatDisplay:15,Color:Show%20Differences,sort_by:,LinkMatePairAligns:false,ShowAlnStat:false,AlignedSeqFeats:false,Label:false%5D">seqgraphic.cgi call with dbname=SRA</a></p>
|
||
|
||
|
||
<p><a href="/projects/sviewer/seqgraphic.cgi?id=nc_000001.10&minheight=220&client=seqviewer&width=1370&from=0&len=249250621&label=Default&color=Color&decor=Default&spacing=Normal&content=Details&tracks=%5Bkey%3Aalignment_track%2Cname%3ASRR505885%2Cdisplay_name%3ASRR505885%2Cid%3ASTD18%2Ccategory%3AAlignments%2Cdbname%3AcSRA%2Cannots%3Ahttp\%3A//ftp-trace.ncbi.nlm.nih.gov/sra/sra-instant/reads/ByRun/sra/SRR/SRR505/SRR505885/SRR505885.sra%2CLayout%3AAdaptiveSeq%2CStatDisplay%3A15%2CColor%3AShow+Differences%2Csort_by%3A%2CLinkMatePairAligns%3Afalse%2CShowAlnStat%3Afalse%2CAlignedSeqFeats%3Afalse%2CLabel%3Afalse%5D">seqgraphic.cgi call with dbname=cSRA</a></p>
|
||
|
||
|
||
<h2 id="bookmark10E">Alignment tracks from AlignDb</h2>
|
||
|
||
|
||
<p>To use internal NCBI AlignDb as data source for alignment track following parameters are required:</p>
|
||
|
||
|
||
<p><strong>key:alignment_track</strong> - to specify the track type as alignment,</p>
|
||
|
||
|
||
<p><strong>annots:AlignDb</strong> - to specify the data source - AlignDb. Capitalization is important and should be exactly as in this example,</p>
|
||
|
||
|
||
<p><strong>batch</strong> - batch number to get the data from.</p>
|
||
|
||
|
||
<h4 id="example">Example</h4>
|
||
|
||
|
||
<p><a href="/projects/sviewer/?id=NC_010453.5&tracks=[key:sequence_track][key:alignment_track,annots:AlignDb,batch:114783]">Assembly to assembly alignment</a></p>
|
||
|
||
|
||
<h3 id="bookmark10C">Remote (HTTP-based) BAM files</h3>
|
||
|
||
|
||
<p>The HTTP and HTTPS protocols are supported for all remote file types. Note: BAM files hosted on the FTP protocol are not supported. To request streaming support for additional file types (e.g. tabixVCF), click the "Support Center" link located at the lower right of the Sequence Viewer page. </p>
|
||
|
||
|
||
<p>Minimal set of parameters to display a BAM alignment track:</p>
|
||
|
||
|
||
<table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>key</th>
|
||
<th>values</th>
|
||
</tr>
|
||
<tr>
|
||
<td>key</td>
|
||
<td>alignment_track</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">dbname</td>
|
||
<td bgcolor="#d2dfed">cSRA</td>
|
||
</tr>
|
||
<tr>
|
||
<td>annots</td>
|
||
<td>path to the remote BAM file (index files is expected to reside at the same path)</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
|
||
|
||
<p>Optional parameters:</p>
|
||
|
||
|
||
<table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>Key</th>
|
||
<th>Value</th>
|
||
<th>Description</th>
|
||
</tr>
|
||
<tr>
|
||
<td>layout</td>
|
||
<td>Adaptive (default)|Packed|Full</td>
|
||
<td>Adaptive - let sviewer decide when to switch between coverage graph, pileup graph and reads<br />Packed - show only coverage or pileup graphs<br>Full - Show reads as lons many reads as possible</br></td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">display_name</td>
|
||
<td bgcolor="#d2dfed">string</td>
|
||
<td bgcolor="#d2dfed">Use defined track name</td>
|
||
<tr>
|
||
<td>ShowAlnStat</td>
|
||
<td>false (default)|true</td>
|
||
<td>Set to always show read's pileup graph</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">GraphHeight</td>
|
||
<td bgcolor="#d2dfed">number</td>
|
||
<td bgcolor="#d2dfed">Graph's height</td>
|
||
</tr>
|
||
</tr></tbody>
|
||
</table>
|
||
|
||
|
||
<h4 id="examples_1">Examples</h4>
|
||
|
||
|
||
<p><a href="/projects/sviewer/?id=NC_005100.4&tracks=[key:alignment_track,display_name:Example1,dbname:cSRA,annots:http\://rgd.mcw.edu/jbrowse/data_rgd6/RNAseq/phenogen/SHR.Brain.totalRNA.rn6.bam,Layout:Adaptive,ShowAlnStat:true,GraphHeight:60]&assm_context=GCF_000001895.5&v=141086500:141092500">Rattus norvegicus strain mixed chromosome 1, Rnor_6.0</a></p>
|
||
|
||
|
||
<p><a href="/projects/sviewer/?id=NC_000023&tracks=[key:alignment_track,display_name:Example2,dbname:cSRA,annots:https\://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/phase3/data/HG00096/high_coverage_alignment/HG00096.wgs.ILLUMINA.bwa.GBR.high_cov_pcr_free.20140203.bam,Layout:Adaptive,ShowAlnStat:true,GraphHeight:60]&v=61691638:61691795">Homo sapiens chromosome X, GRCh38.p7 Primary Assembly</a></p>
|
||
|
||
|
||
<p><a href="/projects/sviewer/BAMDemo.html">Remote (HTTP-hosted) BAM files visualization demo</a></p>
|
||
|
||
|
||
<h3 id="bookmark10d">BigBED and BigWIG files</h3>
|
||
|
||
|
||
<p>The FTP protocol is supported for bigBED and bigWIG files.</p>
|
||
|
||
|
||
<p>Embedding for BigBED and BigWIG tracks is done the same way as with any other files. User needs to specify corresponding dbname and annots parameters:</p>
|
||
|
||
|
||
<table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>Key</th>
|
||
<th>Value</th>
|
||
<th>Description</th>
|
||
</tr>
|
||
<tr>
|
||
<td>dbname</td>
|
||
<td>BigWig|BigBed</td>
|
||
<td>bigWig or bigBed for corresponding type of data</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">annot</td>
|
||
<td bgcolor="#d2dfed">string</td>
|
||
<td bgcolor="#d2dfed">Location of the file on the web, http or ftp protocol</td>
|
||
</tr></tbody>
|
||
</table>
|
||
|
||
|
||
<h4 id="examples_2">Examples</h4>
|
||
|
||
|
||
<p><strong>annots usage example</strong>: http\://hgdownload.soe.ucsc.edu/hubs/gtexAnalysis/hg38/gtexAwgAseDensity.bw</p>
|
||
|
||
|
||
<p><a href="/projects/sviewer/embedded_big_wig_bed.html">SV Demo</a></p>
|
||
|
||
|
||
<h3 id="bookmark11">Appendix A: Tracks Parameters</h3>
|
||
|
||
|
||
<p>The ‘tracks’ parameters are for advanced developers.</p>
|
||
|
||
|
||
<h3 id="bookmark12">‘Tracks’ parameter syntax:</h3>
|
||
|
||
|
||
<p>The ‘tracks’ parameter is used to configure track content, track order, and track display in the rendered image. The track display includes track rendering options and other track-specific settings. The syntax for “tracks” parameter is:</p>
|
||
|
||
|
||
<p>tracks=[track1 ][track2][…]</p>
|
||
|
||
|
||
<ol>
|
||
<li>The settings for one track are grouped together using a pair of square brackets ‘[‘ and ‘]’.</li>
|
||
<li>The order of tracks in the list determines the final track order in the rendered image.</li>
|
||
</ol>
|
||
|
||
|
||
<p>There can be a special track definition in tracks parameter (must be the first track) - <strong>[amend]</strong>. If present, track definitions in the URL will be merged with discovered/TMS tracks. If absent, only tracks in the URL will be shown. Compare <a href="/projects/sviewer/?id=NC_000021">predefined default tracks</a>, <a href="/projects/sviewer/?id=NC_000021&tracks=[id:T1444028]">the track given in the URL</a>, and <a href="/projects/sviewer/?id=NC_000021&tracks=[amend][id:T1444028]">both predefined and URL tracks</a>.</p>
|
||
|
||
|
||
<p>The format of settings for each track grouped in one pair of ‘[‘ and ‘]’ is:</p>
|
||
|
||
|
||
<p><strong>key</strong> :track_key [, <strong>subkey</strong> :feature_subtype]
|
||
[, <strong>name</strong> :track_name]
|
||
[, <strong>display_name</strong> :track_title]
|
||
[, <strong>annots</strong> :annot1[|annot2]]
|
||
[, <strong>shown</strong> :true/false]
|
||
[, <strong>comments</strong> :comment1|loc1[|comment2|loc2]]
|
||
[, <strong>highlights</strong> :label1|...|[labelN]|[GeneID\:id1]|...|[GeneID\:idM]]
|
||
[, <strong>highlights_color</strong> :color]
|
||
[, <strong>filter</strong> :A>aaa and B<bbb and (C eq ccc or D<=ddd)]
|
||
[, <strong>sort_by</strong> :sorting criteria]
|
||
[, <strong>track_setting_key </strong>:value]<strong><em>*
|
||
</em>*HighlightMode:value]</strong>
|
||
<span style="line-height: 20.4px;"> [, </span>
|
||
The track settings consist of a set of key:value pairs. Any unmatched pair (only key or value) will be ignored. A key:value pair is formed using ‘:’, and multiple key:value pairs are separated by ‘,’.</p>
|
||
|
||
|
||
<p>[ <strong>Note</strong> ] Since these five special characters ([],|:) are used as delimiters in ‘tracks’ parameter, if any of the five special characters are used in user-provided name, title or comment, they have to be escaped using a backslash (‘\’).</p>
|
||
|
||
|
||
<ol>
|
||
<li>
|
||
<p><strong>key</strong> is required. It is one of the predefined track type keys. The same key can be used in multiple track instances. Track keys are case-sensitive. The existing track keys are:</p>
|
||
<ul>
|
||
<li>sequence_track</li>
|
||
<li>six_frames_translation</li>
|
||
<li>SNP_track</li>
|
||
<li>HapMapRR_track</li>
|
||
<li>SNP_Bins_track</li>
|
||
<li>segment_map_track</li>
|
||
<li>graph_track</li>
|
||
<li>graph_overlay</li>
|
||
<li>gene_model_track</li>
|
||
<li>alignment_track</li>
|
||
<li>feature_track</li>
|
||
<li>dbvar_track</li>
|
||
<li>user_data_track</li>
|
||
<li>trace_track</li>
|
||
</ul>
|
||
</li>
|
||
<li>
|
||
<p><strong>subkey</strong> is required only when key is a feature_track. It is the storage key for a given feature subtype, such as STS, repeat_region, misc_feature and Protein. For a complete list of feature subtype storage keys, please refer to Appendix A.</p>
|
||
</li>
|
||
<li><strong>name</strong> is optional. However, if two or more track instances use the same track key (and subkey combination), then track name (any unique arbitrary track name) is necessary to uniquely represent a track instance.</li>
|
||
<li><strong>display_name</strong> is optional. It is used for display purpose, such as track title in the rendered image and track name in track configurator. If display_name is not provided, a default display name will be generated based on information retrieved from data. The defined order of precedence is annotation title, annotation name, and file name for uploaded data.</li>
|
||
<li><strong>annots</strong> is optional. It lists all the annotations needed to be shown in the given track type. If there is more than one annotation, the annotations are separated using '|'. If it is absent, all annotations related to the track type will be loaded. The order of annotations in the list determines the subtrack (each for one annotation) order in the rendered image. If the annotation is unnamed, then the annotation name should be “Unnamed”.</li>
|
||
<li>
|
||
<p><strong>comments</strong> is optional. Comments are used for highlighting one or more specific locations in a track. A comment has to come with a pair of comment text and location separated using ‘|’, such as comments:comment1|position1. The sequence location is an integer. ‘,’ separated locations are not acceptable. Multiple comments are supported that are also separated using ‘|’, such as comments:comment1|pos1| comment2|pos2. Figure 2 shows an example with multiple comments specified.</p>
|
||
<p><img src="/core/assets/sequence-viewer/images/Image_013.jpg" alt="image13" />
|
||
<em>Figure 2. Example screenshots for ‘tracks’ parameter with ‘comments’ specified. The ‘tracks’ parameter used in the example is:</em></p>
|
||
<p><em>tracks=[key:gene_model_track,comments:comment 1|28000|comment 2|48000] [key:feature_track,subkey:STS,comments:histogram comment 1|20000|histogram comment 2|35000|histogram comment 3|44000]</em></p>
|
||
</li>
|
||
<li>
|
||
<p><strong>highlights</strong> is optional and not all track types support this setting. When specified, it highlights one or more objects:</p>
|
||
<ul>
|
||
<li>represented using the exactly same labels as the ones shown on screen (case-insensitive)</li>
|
||
<li>gene(s), having the GeneID(s), listed in the <strong>highlights</strong> parameter</li>
|
||
</ul>
|
||
<p>If multiple objects need to be highlighted their labels and/or GeneIDs should be separated using '|', such as highlights:label1|label2.
|
||
The colon after the GeneID identifier needs to be prefixed with '\', such as highlights:GeneID\:100506658.
|
||
The highlighted objects will be promoted to the top row in the corresponding track to make it more prominent, will be rendered as the normal size even in zoomed-out mode that other objects are shown in a reduced size, and will be shown with label enabled if the label fits.</p>
|
||
<p>The currently supported tracks types include: gene_model_track, feature_track, dbvar_track, and segment_map_track. Figure 3 shows an example with multiple highlighted objects specified:</p>
|
||
<p><img src="/core/assets/sequence-viewer/images/Image_014.jpg" alt="image14" />
|
||
<em>Figure 3. Example screenshots for ‘tracks’ parameter with ‘highlighs’ specified. The ‘tracks’ parameter used in the example is:</em></p>
|
||
<p><em>tracks=[key:sequence_track] [key:SNP_track] [key:gene_model_track,annots:Unnamed][key:dbvar_track,name:dbvar_track1,annots:NA000001999.1,Rendering:Default,highlights:nsv492962|nssv579665]</em></p>
|
||
</li>
|
||
<li>
|
||
<p><strong>highlights_color</strong> is optional. When specified, it defines the color to be used for highlights in the curent track. Accepted formats:</p>
|
||
<ul>
|
||
<li>A named color, such as "red", "blue", "salmon", etc. Supports <a href="http://www.w3schools.com/colors/colors_names.asp">HTML color names</a></li>
|
||
<li><span style="line-height: 20.4px;"> HTML-format colors, such as "#f0f0dd", or "f0f0dd". These are accepted with or without the leading '#'. </span>
|
||
The color used for highlighting can be changed for all tracks using the global <strong>highlights_color</strong> parameter.</li>
|
||
</ul>
|
||
</li>
|
||
<li><strong>filter</strong> is optional and not all track types support this setting. When specified, it only shows the objects that get passed through the filter. The filter string is similar to many other query languages. For example, if A, B, C, D and E are identifiers, it is ok to have A > aaa and B < bbb and (C eq ccc or D >=ddd) or E between 2 and 10. Currently, the supported operators include: and, or, xor, sub, not, like, between, in, eq, >, <, >=, and <=.</li>
|
||
<li><strong>sort_by</strong> is optional and not all track types support this setting. When specified, it sorts the objects into several sub-tracks/sub-groups according to a predefined sorting criteria within a given track.</li>
|
||
<li>
|
||
<p><strong>track_setting_key</strong> :value pairs are track-specific. The currently exposed track-specific settings include:</p>
|
||
<h4 id="bookmark15">key: six_frames_translation</h4>
|
||
<p><table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>key_name</th>
|
||
<th>value</th>
|
||
<th>comment</th>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="4">ShowOption Default: All</td>
|
||
<td bgcolor="#d2dfed">Forward</td>
|
||
<td bgcolor="#d2dfed">Show forward direction translations (+1, +2, +3)</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Reverse</td>
|
||
<td>Show reverse direction translations (-1, -2, -3)</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">LTR</td>
|
||
<td bgcolor="#d2dfed">Show translations from left to right (sense strand) regardless of sequence orientation</td>
|
||
</tr>
|
||
<tr>
|
||
<td>All</td>
|
||
<td>Show all six-frame translations</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="5">Orfthreshold Default: 20</td>
|
||
<td style="background-color: rgb(210, 223, 237);">0</td>
|
||
<td style="background-color: rgb(210, 223, 237);">Highlight all ORFs</td>
|
||
</tr>
|
||
<tr>
|
||
<td>20</td>
|
||
<td>Highlight ORFs equal or longer than 20 codons</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="background-color: rgb(210, 223, 237);">100</td>
|
||
<td style="background-color: rgb(210, 223, 237);">Highlight ORFs equal or longer than 100 codons</td>
|
||
</tr>
|
||
<tr>
|
||
<td>250</td>
|
||
<td>Highlight ORFs equal or longer than 250 codons</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="background-color: rgb(210, 223, 237);">100000000</td>
|
||
<td style="background-color: rgb(210, 223, 237);">Do not highlight ORFs</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="2">HighlightCodons<br />Default: true</td>
|
||
<td>true</td>
|
||
<td>Highligh start and stop codons</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="background-color: rgb(210, 223, 237);">false</td>
|
||
<td style="background-color: rgb(210, 223, 237);">Don’t highligh start and stop codons</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
<h4 id="bookmark16">key:alignment_track</h4>
|
||
<p><table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>key_name</th>
|
||
<th>value</th>
|
||
<th>comment</th>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="16">Color<br />Default: Show Differences</td>
|
||
<td bgcolor="#d2dfed">Column Quality score<br />– DNA</td>
|
||
<td bgcolor="#d2dfed">DNA: Score residues based on how well a particular residue agrees with the others in a column.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Frequency-Based Difference</td>
|
||
<td>DNA/Protein: Score residues based on their frequency in the column</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Show Differences</td>
|
||
<td bgcolor="#d2dfed">DNA/Protein: Score residues based on match/mismatch to a master/anchor row</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Nucleic Acid Colors</td>
|
||
<td>DNA: Assign color based on residue (A - Red, G - Blue, C - Yellow, T - Green)</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Column Quality score - Protein</td>
|
||
<td bgcolor="#d2dfed">Protein: Score residues based on how well a particular residue agrees with the others in a column.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Rasmol Amino Acid Colors</td>
|
||
<td>Protein: Used by the application RasMol to group amino acids with similar properties</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Shapely Amino Acid Colors</td>
|
||
<td bgcolor="#d2dfed">Protein: Used by the application RasMol to group amino acids with similar shapes using a standard color table</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BLOSUM45</td>
|
||
<td>Protein: Matrix made by matblas from blosum45.iij BLOSUM Clustered Scoring Matrix in 1/3 Bit Units</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">BLOSUM62</td>
|
||
<td bgcolor="#d2dfed">Protein: Matrix made by matblas from blosum62.iij BLOSUM Clustered Scoring Matrix in 1/2 Bit Units</td>
|
||
</tr>
|
||
<tr>
|
||
<td>BLOSUM80</td>
|
||
<td>Protein: Matrix made by matblas from blosum80.iij BLOSUM Clustered Scoring Matrix in 1/2 Bit Units</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Protein Quality Scoring with Coloring</td>
|
||
<td bgcolor="#d2dfed">Protein: Color residues where the quality scoring is above (or below) a given threshold</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Hydropathy Scale</td>
|
||
<td>Protein: Side chain hydropathy, corrected for solvation</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Membrane preference</td>
|
||
<td bgcolor="#d2dfed">Protein: Membrane-buried preference parameters</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Signal sequence</td>
|
||
<td>Protein: Signal sequence helical potential</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Size</td>
|
||
<td bgcolor="#d2dfed">Protein: Amino acid size</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>Disable alignment score coloration</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="2">AlignedSeqFeats<br />Default: false</td>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">Show features projected from the aligned sequences</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>Don’t show features projected from the aligned sequences</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="2">Label<br />Default: true</td>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">Show labels for alignments</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>Hide labels for alignments</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="2">ShowAligns<br />Default: true</td>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">Show alignments always</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>Hide alignments when alignment statistics are shown</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="2">ShowSecondPass<br />Default: true</td>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">Show second-pass aligments</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>Hide second-pass aligments</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="8">Layout Default:<br />Adaptive1000</td>
|
||
<td bgcolor="#d2dfed">Adaptive200</td>
|
||
<td bgcolor="#d2dfed">Show the individual alignments if less than 200 alignments. Otherwise smear the alignments.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Adaptive1000</td>
|
||
<td>Show the individual alignments if less than 1000 alignments. Otherwise smear the alignments.</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Adaptive5000</td>
|
||
<td bgcolor="#d2dfed">Show the individual alignments if less than 5000 alignments. Otherwise smear the alignments.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Adaptive20000</td>
|
||
<td>Show the individual alignments if less than 20000 alignments. Otherwise smear the alignments.</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Adaptive100000</td>
|
||
<td bgcolor="#d2dfed">Show the individual alignments if less than 100000 alignments. Otherwise smear the alignments.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Adaptive250000</td>
|
||
<td>Show the individual alignments if less than 250000 alignments. Otherwise smear the alignments.</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Expanded by position</td>
|
||
<td bgcolor="#d2dfed">Show one alignment per row sorted by alignments' start location</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Smear</td>
|
||
<td>Smear all alignments into a smear bar</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="9">StatDisplay<br />Default: -1</td>
|
||
<td bgcolor="#d2dfed">-1</td>
|
||
<td bgcolor="#d2dfed">Don't show alignment statistics</td>
|
||
</tr>
|
||
<tr>
|
||
<td>8</td>
|
||
<td>Show A, T, G, C, and gaps percentage as table</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">9</td>
|
||
<td bgcolor="#d2dfed">Show A, T, G, C, and gaps percentage as bar graph</td>
|
||
</tr>
|
||
<tr>
|
||
<td>10</td>
|
||
<td>Show A, T, G, C, and gaps count as table</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">11</td>
|
||
<td bgcolor="#d2dfed">Show A, T, G, C, and gaps count as bar graph</td>
|
||
</tr>
|
||
<tr>
|
||
<td>12</td>
|
||
<td>Show matches, mismatches, and gaps percentage as table</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">13</td>
|
||
<td bgcolor="#d2dfed">Show matches, mismatches, and gaps percentage as bar graph</td>
|
||
</tr>
|
||
<tr>
|
||
<td>14</td>
|
||
<td>Show matches, mismatches, and gaps count as table</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">15</td>
|
||
<td bgcolor="#d2dfed">Show matches, mismatches, and gaps count as bar graph</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="3">UnalignedTailsMode<br />Default:glyph</td>
|
||
<td>glyph</td>
|
||
<td>Show length of unaligned tails</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">hide</td>
|
||
<td bgcolor="#d2dfed">Hide tails</td>
|
||
</tr>
|
||
<tr>
|
||
<td>sequence</td>
|
||
<td>Show sequence of unaligned tails</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="3">Sort_by<br />Default: </td>
|
||
<td bgcolor="#d2dfed">strand</td>
|
||
<td bgcolor="#d2dfed">Alignment strand</td>
|
||
</tr>
|
||
<tr>
|
||
<td>haplotype</td>
|
||
<td>Haplotype (if available)</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">reciprocity</td>
|
||
<td bgcolor="#d2dfed">Reciprocity score (if available)</td>
|
||
</tr>
|
||
<tr>
|
||
<td>GraphHeight</td>
|
||
<td>Numeric value</td>
|
||
<td>This parameter is applicable to coverage or pile-up graph of BAM/CSRA alignments</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">GraphColor</td>
|
||
<td bgcolor="#d2dfed">Color name or HTML color code</td>
|
||
<td bgcolor="#d2dfed">This parameter is applicable to coverage or pile-up graph of BAM/CSRA alignments</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
<h4 id="bookmark17">key:gene_model_track</h4>
|
||
<p><table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>key_name</th>
|
||
<th>values</th>
|
||
<th>comment</th>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="6">Options<br />Default:MergePairs</td>
|
||
<td bgcolor="#d2dfed">GeneOnly</td>
|
||
<td bgcolor="#d2dfed">Only the 'green' gene bar is shown</td>
|
||
</tr>
|
||
<tr>
|
||
<td>MergeAll</td>
|
||
<td>Merge all transcripts and CDSs into a single line, no gene bar shown.</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">MergePairs</td>
|
||
<td bgcolor="#d2dfed">Merge the display of the transcript and its coding region as appropritate. Coding reginos are represented by different color. No gene bar is shown.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>ShowAllButGenes</td>
|
||
<td>Show all transcripts and CDSs separately but with no gene bar.</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">ShowAll</td>
|
||
<td bgcolor="#d2dfed">Show all transcripts and CDSs separately with gene bar.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>SingleLine</td>
|
||
<td>No gene bar, but merge exon/CDS features and only show on a single line.</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="2">HideNonCoding<br />Default: false</td>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">Show only transcripts or gene loci with associated CDS</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>Show both coding and non-coding features</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="2" bgcolor="#d2dfed">HideModels<br />Default: false</td>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">Do not show predicted RefSeq models from Gnomon</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>Show model and curated RefSeq variants</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="2">CCDSOnly<br />Default: false</td>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">Show only CCDS variants</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>Show CCDS and non-CCDS variants</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="2" bgcolor="#d2dfed">SelectOnly<br />Default: false</td>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">Show only RefSeq Select or MANE Select variants</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>Do not limit to RefSeq Select or MANE Select variants</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="2">SNPs<br />Default: false</td>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">Show SNP features projected from RNA and coding region features</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>Don’t show SNP features projected from RNA and coding region features</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="2" bgcolor="#d2dfed">CDSProductFeats<br />Default: false</td>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">Show product features projected from protein sequence</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>Don’t show product features projected from protein sequence</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="2">ShowLabelsForAllFe atures<br />Default: false</td>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">For top labeling, show labels for all features inside one gene model. This affects the top label mode only.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>false</td>
|
||
<td>For top labeling, show labels for the first gene, RNA and coding region only in one gene model. This affects the top label mode only.</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
<h4 id="bookmark18">key:SNP_track</h4>
|
||
<p><table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>key_name</th>
|
||
<th>value</th>
|
||
<th>comment</th>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="4">Layout<br />Default: Adaptive</td>
|
||
<td bgcolor="#d2dfed">Adaptive</td>
|
||
<td bgcolor="#d2dfed">Show labels if less than 15 variants; Show density bar if greater than 50 variants</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Density</td>
|
||
<td>Always show the density bar of variants</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Features</td>
|
||
<td bgcolor="#d2dfed">Show all variants rendered individually</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Labels</td>
|
||
<td>Always show the labels of variants</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
<h4 id="bookmark19">key:feature_track</h4>
|
||
<p><table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>key_name</th>
|
||
<th>value</th>
|
||
<th>comment</th>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="3">Layout<br />Default: Adaptive</td>
|
||
<td bgcolor="#d2dfed">Packed</td>
|
||
<td bgcolor="#d2dfed">Track is displayed, with all features collapsed on a single line.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Adaptive</td>
|
||
<td>show the individual features if less than 50 features. Otherwise, show histogram.</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Layered</td>
|
||
<td bgcolor="#d2dfed">Always show the individual features and layer the features in a compact form</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="5">LinkedFeat <br /> Default:Packed</td>
|
||
<td>Default</td>
|
||
<td>All features, both parent and all child features</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Packed</td>
|
||
<td bgcolor="#d2dfed">Show parent on one line and all children merged below it.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>ParentHidden</td>
|
||
<td>Show only the children, not parent</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Hidden</td>
|
||
<td bgcolor="#d2dfed">Show the parent features, not the children</td>
|
||
</tr>
|
||
<tr>
|
||
<td>OnParent</td>
|
||
<td>Render all child features on the parent feature</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Sort_by</td>
|
||
<td bgcolor="#d2dfed" colspan="2">Supported sort_by includes: concordancy, apply to clone features only</td>
|
||
</tr>
|
||
<tr>
|
||
<td rowspan="2">sort_reads<br />Default: false</td>
|
||
<td>false</td>
|
||
<td>do not sort intron features track by number of spliced reads</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">sort intron features track by number of spliced reads, with features with most spliced reads at the top</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="2">sort_strands<br />Default: false</td>
|
||
<td>false</td>
|
||
<td>do not sort intron features track by strand</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">true</td>
|
||
<td bgcolor="#d2dfed">features on the forward strand are sorted separately from features on the reverse strand</td>
|
||
</tr>
|
||
<tr>
|
||
<td>read_range, intron features track only</td>
|
||
<td>min|max <br /> Default: inf|inf </td>
|
||
<td>min - number or 'inf'=0, Minimum threshold, the values below this threshold will be hidden from view<br /><br /> max - number or 'inf'=infinity, Maximum threshold, the values above this threshold will be hidden from view <br />
|
||
</td></tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
<h4 id="bookmark19a">key:aggregate_feature_track</h4>
|
||
<p><table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>key_name</th>
|
||
<th>value</th>
|
||
<th>comment</th>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="3">subkey</td>
|
||
<td bgcolor="#d2dfed">biological_region</td>
|
||
<td bgcolor="#d2dfed">
|
||
<p>Shows the following set of features:</p>
|
||
<ul>
|
||
<li>miscellaneous features</li>
|
||
<li>recombination features</li>
|
||
<li>sequence secondary structures</li>
|
||
<li>mobile genetic elements</li>
|
||
<li>protein binding sites</li>
|
||
<li>origin of replications</li>
|
||
<li>repeat regions</li>
|
||
<li>stem loops</li>
|
||
<li>regulatory features</li>
|
||
</ul>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>aggregate_features</td>
|
||
<td>A track combining all possible features</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
<p>The aggregate_feature_track supports all parameters, supported by the feature track.</p>
|
||
<h4 id="bookmark20">key:dbvar_track</h4>
|
||
<p><table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>key_name</th>
|
||
<th>value</th>
|
||
<th>comment</th>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed" rowspan="6">Rendering<br />Default: Packed</td>
|
||
<td bgcolor="#d2dfed">Default</td>
|
||
<td bgcolor="#d2dfed">All features, both parent and all child features</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Packed</td>
|
||
<td>Show parent on one line and all children merged below it.</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">ParentHidden</td>
|
||
<td bgcolor="#d2dfed">Show only the supporting variants (children) not the variant region (parent)</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Hidden</td>
|
||
<td>Show the variant region (parent) not the supporting variants (children)",</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">SingleLine</td>
|
||
<td bgcolor="#d2dfed">Track is displayed, with all features collapsed on a single line.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Histogram</td>
|
||
<td>Track is displayed, with all features displayed as a histogram.</td>
|
||
</tr>
|
||
<tr>
|
||
<td>Filter</td>
|
||
<td bgcolor="#d2dfed" colspan="2">Supported filters include: variant_quality=low/high, pilot=1/2, len=size, clinical_assertion= likely_unknown/benign/likely_benign/pathogenic/likely_pathogenic/not_tested/oth er,sampleset_type=case/control</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">Sort_by</td>
|
||
<td colspan="2">Supported sort_by:<ul id="l13"><li>Variant_quality</li><li>pilot</li><li>clinical_assertion</li><li>sampleset_type</li><li>validation_status</li></ul></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
<h4 id="bookmark20a">key:graph_track</h4>
|
||
<p><table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>key_name</th>
|
||
<th colspan="2">value</th>
|
||
<th colspan="3">comment</th>
|
||
</tr>
|
||
<tr>
|
||
<td>color</td>
|
||
<td bgcolor="#d2dfed" colspan="2">It can be color name such as 'red', 'dark blue', or RGB color such as '255 0 0', or HTML color code such as '#FF0000'<br />Default: blue</td>
|
||
<td colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">neg_color</td>
|
||
<td colspan="2">Color for negative values<br />Default: deep red</td>
|
||
<td bgcolor="#d2dfed" colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td>height</td>
|
||
<td bgcolor="#d2dfed" colspan="2">Graph height in pixels. Default value is 30 pixels for histogram and line graph, and 10 pixels for smear bar</td>
|
||
<td colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">style</td>
|
||
<td colspan="2">Graph rendering styles:<ul style="line-height: 20.3999996185303px;"><li>histogram</li><li>line graph</li><li>smear bar</li></ul><br />Default: histogram</td>
|
||
<td bgcolor="#d2dfed" colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td>num bins</td>
|
||
<td bgcolor="#d2dfed" colspan="2">Integer from 2 to 10</td>
|
||
<td colspan="3">Smear bar is a heat map of data values from min value colored as light blue to the max value colored as dark blue.<br />The coloring can be controlled by num_bins parameter. Num_bins parameter allows to partition the data into the number of equal bins</td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">scale</td>
|
||
<td colspan="2">What scale to use:<ul style="line-height: 20.3999996185303px;"><li>linear</li><li>log 2</li><li>log 10</li><li>loge</li></ul><br />Default: linear</td>
|
||
<td bgcolor="#d2dfed" colspan="3"></td>
|
||
</tr>
|
||
<tr>
|
||
<td>stored_scale</td>
|
||
<td bgcolor="#d2dfed" colspan="2">Scale of stored data:<br /><ul style="line-height: 20.3999996185303px;"><li>linear</li><li>log2</li><li>log10</li><li>loge</li></ul></td>
|
||
<td colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">ocolor</td>
|
||
<td colspan="2">Color to use for outliers<br />Default: red</td>
|
||
<td bgcolor="#d2dfed" colspan="3"></td>
|
||
</tr>
|
||
<tr>
|
||
<td>uid</td>
|
||
<td bgcolor="#d2dfed" colspan="2">User ID. Any alphanumeric value that uniquely identifies the track.<br />Default: none</td>
|
||
<td colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">opacity</td>
|
||
<td colspan="2">Color opacity in a percentage value (100 completely visible)<br />Default: 100</td>
|
||
<td bgcolor="#d2dfed" colspan="3"></td>
|
||
</tr>
|
||
<tr>
|
||
<td>range</td>
|
||
<td bgcolor="#d2dfed" colspan="2">min|max|auto</td>
|
||
<td colspan="3">min - real number or 'inf', Minimum threshold, the values below this threshold will be clipped<br /><br /> max - real number or 'inf', Maximum threshold, the values above this threshold will be clipped<br /> <br />auto - optional flag indicating that value range should be calculated automatically</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
<h4 id="bookmark20b">key:graph_overlay</h4>
|
||
<p>The graph_overlay key allows multiple graph tracks with the same data dimensions to be overlaid in a single track. The tracks to overlay are indicated by the ‘subtracks’ parameter.</p>
|
||
<p><table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>key_name</th>
|
||
<th colspan="2">value</th>
|
||
<th colspan="3">comment</th>
|
||
</tr>
|
||
<tr>
|
||
<td>subtracks</td>
|
||
<td bgcolor="#d2dfed" colspan="2">List of tracks to be included in graph overlay. The values represent track_ids - strings separated by ‘|’. For example: track1| track2| track3. Track_ids are references to the other tracks and can be either annot name, id parameter or uid parameter.<br />Default: Packed</td>
|
||
<td colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">BG</td>
|
||
<td colspan="2">Background color. It can be color name such as 'red', 'dark blue', or RGB such as '255,0,0', or HTML color code as '#FF0000'<br />Default: white</td>
|
||
<td bgcolor="#d2dfed" colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td>height</td>
|
||
<td bgcolor="#d2dfed" colspan="2">Graph height in pixels<br />Default: 30</td>
|
||
<td colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">scale</td>
|
||
<td colspan="2">What scale to use<ul><li>linear</li><li>log2</li><li>log10</li><li>loge</li></ul><br />Default: linear</td>
|
||
<td bgcolor="#d2dfed" colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td>stored_scale</td>
|
||
<td bgcolor="#d2dfed" colspan="2">Scale of stored data<ul><li>linear</li><li>log2</li><li>log10</li><li>loge</li></ul><br />Default: linear</td>
|
||
<td colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td bgcolor="#d2dfed">ocolor</td>
|
||
<td colspan="2">Color to use for outliners<br />Default: red</td>
|
||
<td bgcolor="#d2dfed" colspan="3"> </td>
|
||
</tr>
|
||
<tr>
|
||
<td>range</td>
|
||
<td bgcolor="#d2dfed" colspan="2">min|max|auto</td>
|
||
<td colspan="3">min - real number or 'inf', Minimum threshold, the values below this threshold will be clipped<br /><br /> max - real number or 'inf', Maximum threshold, the values above this threshold will be clipped<br /> <br />auto - optional flag indicating that value range should be calculated automatically</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
<p>Example:
|
||
<a href="/projects/sviewer/?id=NC_000001.10&v=151955200-151956000&tracks=%5Bkey:graph_track,annots:NA000011424.1,opacity:50,color:navy,shown:false%5D%5Bkey:graph_track,annots:NA000011426.1,opacity:50,color:tomato,shown:false%5D%5Bkey:graph_track,annots:NA000011432.1,color:deeppink,opacity:50,shown:false%5D%5Bkey:graph_overlay,subtracks:NA000011424.1%7CNA000011426.1%7CNA000011432.1,height:120,display_name:overlay%20example%5D">http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_000001.10&v=151955200-151956000&tracks=[key:graph_track,annots:NA000011424.1,opacity:50,color:navy,shown:false][key:graph_track,annots:NA000011426.1,opacity:50,color:tomato,shown:false][key:graph_track,annots:NA000011432.1,color:deeppink,opacity:50,shown:false][key:graph_overlay,subtracks:NA000011424.1|NA000011426.1|NA000011432.1,height:120,display_name:overlay%20example]</a></p>
|
||
<p>In the example above graph overlay track
|
||
<em>[key:graph_overlay,subtracks:NA000011424.1|NA000011426.1|NA000011432.1,height:120,display_name:overlay example]</em>
|
||
refers to three subtracks by their annot names.</p>
|
||
<p>Alternatively, each track can be assigned a user id (uid) and the graph overlay can refer to uid instead
|
||
<em>[key:graph_overlay,subtracks:tr2|tr1|tr3,height:120,display_name:overlay example]</em>
|
||
<a href="/projects/sviewer/?id=NC_000001.10&v=151955200-151956000&tracks=%5bkey:graph_track,annots:NA000011424.1,uid:tr1,opacity:50,color:navy,shown:false%5d%5bkey:graph_track,name:aaa,annots:NA000011426.1,uid:tr2,opacity:50,color:tomato,shown:false%5d%5bkey:graph_track,annots:NA000011432.1,uid:tr3,color:deeppink,opacity:50,shown:false%5d%5bkey:graph_overlay,subtracks:tr2%7Ctr1%7Ctr3,height:120,display_name:overlay%20example">http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NC_000001.10&v=151955200-151956000&tracks=%5bkey:graph_track,annots:NA000011424.1,uid:tr1,opacity:50,color:navy,shown:false%5d%5bkey:graph_track,name:aaa,annots:NA000011426.1,uid:tr2,opacity:50,color:tomato,shown:false%5d%5bkey:graph_track,annots:NA000011432.1,uid:tr3,color:deeppink,opacity:50,shown:false%5d%5bkey:graph_overlay,subtracks:tr2|tr1|tr3,height:120,display_name:overlay%20example</a></p>
|
||
<h4 id="bookmark20c">key:trace_track</h4>
|
||
<p>The trace_track key allows to visualize traces data in NCBI Sequence Viewer.</p>
|
||
<p><table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>key_name</th>
|
||
<th>value</th>
|
||
<th>comment</th>
|
||
</tr>
|
||
<tr>
|
||
<td style="background-color: #d2dfed">style</td>
|
||
<td style="background-color: #d2dfed">curve | intensity</td>
|
||
<td style="background-color: #d2dfed">Trace graph style</td>
|
||
</tr>
|
||
<tr>
|
||
<td>show_conf_graph</td>
|
||
<td style="">true | false</td>
|
||
<td style="">Confidence graph visibility</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="background-color: rgb(210, 223, 237);">height</td>
|
||
<td style="background-color: rgb(210, 223, 237);">70</td>
|
||
<td style="background-color: rgb(210, 223, 237);">Track height</td>
|
||
</tr>
|
||
<tr>
|
||
<td>colorA</td>
|
||
<td>red</td>
|
||
<td>Trace chromatogram for base A</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="background-color: rgb(210, 223, 237);">colorC</td>
|
||
<td style="background-color: rgb(210, 223, 237);">green</td>
|
||
<td style="background-color: rgb(210, 223, 237);">
|
||
<span style="line-height: 20.4px;">Trace chromatogram for base C</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>colorG</td>
|
||
<td>blue</td>
|
||
<td>
|
||
<span style="line-height: 20.4px;">Trace chromatogram for base G</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="background-color: rgb(210, 223, 237);">colorT</td>
|
||
<td style="background-color: rgb(210, 223, 237);">purple</td>
|
||
<td style="background-color: rgb(210, 223, 237);">
|
||
<span style="line-height: 20.4px;">Trace chromatogram for base T</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>colorConfMin</td>
|
||
<td>dark green</td>
|
||
<td>Confidence graph's minimum</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="background-color: rgb(210, 223, 237);">colorConfMax</td>
|
||
<td style="background-color: rgb(210, 223, 237);">light green</td>
|
||
<td style="background-color: rgb(210, 223, 237);">
|
||
<span style="line-height: 20.4px;">Confidence graph's maximum</span>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
</li>
|
||
<li>
|
||
<p><strong>HighlightMode</strong> - defines how genes will be highlighted in overview mode: <table border="1" width="100%">
|
||
<tbody>
|
||
<tr>
|
||
<th>Value</th>
|
||
<th>Description</th>
|
||
<th>Sample output</th>
|
||
</tr>
|
||
<tr>
|
||
<td style="background-color: rgb(210, 223, 237);">0</td>
|
||
<td style="background-color: rgb(210, 223, 237);">Disabled (default)</td>
|
||
<td style="">
|
||
<img src="/core/assets/sequence-viewer/images/highlight-mode-0.png" alt="highlights color sample" />
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>1</td>
|
||
<td>Highlight the top most important genes</td>
|
||
<td style="background-color: #d2dfed">
|
||
<img src="/core/assets/sequence-viewer/images/highlight-mode-1.png" alt="highlights color sample" />
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td style="background-color: rgb(210, 223, 237);">2</td>
|
||
<td style="background-color: rgb(210, 223, 237);">Display the labels of the top most important genes</td>
|
||
<td>
|
||
<img src="/core/assets/sequence-viewer/images/highlight-mode-2.png" alt="highlights color sample" />
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
</li>
|
||
<li>
|
||
<p><strong>label</strong> - label position relative to the feature</p>
|
||
<p>Values (same as in dialog Tools|Preferences|Label Placement):</p>
|
||
<ul>
|
||
<li>Default</li>
|
||
<li>Top label</li>
|
||
<li>Side label</li>
|
||
<li>No label</li>
|
||
</ul>
|
||
<p>An ordinal number (base 0) of the value must be given, not the string.</p>
|
||
</li>
|
||
<li>
|
||
<p><strong>color</strong> - greyscale or colored</p>
|
||
<p>Values (same as in dialog Tools|Preferences|Coloration):</p>
|
||
<ul>
|
||
<li>Color</li>
|
||
<li>Greyscale</li>
|
||
</ul>
|
||
<p>An ordinal number (base 0) of the value must be given, not the string.</p>
|
||
</li>
|
||
<li>
|
||
<p><strong>decor</strong> - feature drawing style</p>
|
||
<p>Values (same as in dialog Tools|Preferences|Shapes):</p>
|
||
<ul>
|
||
<li>Default</li>
|
||
<li>Arrows</li>
|
||
<li>CircleAnchor</li>
|
||
<li>Fancy</li>
|
||
<li>SquareAnchor</li>
|
||
</ul>
|
||
<p>An ordinal number (base 0) of the value must be given, not the string.</p>
|
||
</li>
|
||
<li>
|
||
<p><strong>spacing</strong> - sets vertical spacing between the features</p>
|
||
<p>Values (same as in dialog Tools|Preferences|Spacing):</p>
|
||
<ul>
|
||
<li>Normal</li>
|
||
<li>Compact</li>
|
||
<li>Oversize</li>
|
||
<li>Overview</li>
|
||
</ul>
|
||
<p>An ordinal number (base 0) of the value must be given, not the string.</p>
|
||
</li>
|
||
</ol>
|
||
|
||
|
||
<h3 id="bookmark21">Key:user_data_track</h3>
|
||
|
||
|
||
<p>Unlike other types of track, <strong>user_data_track</strong> is a track key to represent a user-uploaded data track that is stored in a NetCache key. By default, all user-uploaded data tracks will be added to bottom of the view. If a user wants to change that default track order without knowing the data track details such as real track key and annotation name, he/she can specify a ‘tracks’ string that contains ‘ <strong>user_data_track</strong> ’ along with a ‘ <strong>data_key</strong> ’ in a specific track order. The track order for the user data track will be honored just like other tracks. In addition to ‘ <strong>data_key</strong> ’ parameter, several other generic parameters are also supported which include: <strong>shown</strong> , <strong>category</strong> , and <strong>subcategory</strong></p>
|
||
|
||
|
||
<p><table width="100%" border="1">
|
||
<tbody>
|
||
<tr>
|
||
<th>key_name</th>
|
||
<th>value</th>
|
||
<th>comment</th>
|
||
</tr>
|
||
<tr>
|
||
<td>data_key</td>
|
||
<td>A NetCache key</td>
|
||
<td></td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
|
||
|
||
<h3 id="bookmark22">‘tracks’ parameter examples:</h3>
|
||
|
||
|
||
<ol>
|
||
<li>
|
||
<p>show sequence track, SNP track, gene model track and alignment tracks
|
||
<strong>“track” parameter:</strong></p>
|
||
<p>tracks=[key:sequence_track][key:SNP_track]
|
||
[key:gene_model_track,annots:Unnamed,Options:ShowAll,SNPs:true]
|
||
[key:alignment_track]</p>
|
||
<p><strong>Full SV link:</strong>
|
||
<a href="https://www.ncbi.nlm.nih.gov/projects/sviewer/?id=nc_000001&tracks=%5Bkey:sequence_track%5D%5Bkey:SNP_track%5D%5Bkey:gene_model_track,annots:Unnamed,Options:ShowAll,SNPs:true%5D%5Bkey:alignment_track%5D&v=180m..181m">http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=nc_000001&tracks=%5Bkey:sequence_track%5D%5Bkey:SNP_track%5D%5Bkey:gene_model_track,annots:Unnamed,Options:ShowAll,SNPs:true%5D%5Bkey:alignment_track%5D&v=180m..181m</a></p>
|
||
</li>
|
||
<li>
|
||
<p>show sequence track, SNP track, gene model track and two dbvar tracks with named annotation accessions
|
||
<strong>“track” parameter:</strong></p>
|
||
<p>tracks=[key:sequence_track][key:SNP_track]
|
||
[key:gene_model_track,annots:Unnamed]
|
||
[key:dbvar_track,name:dbvar_track1,annots:NA000001999.1|NA000002000.1,Rendering:Default]
|
||
[key:dbvar_track,dbvar_track2,annots:NA000002001.1,Rendering:SingleLine]</p>
|
||
<p><strong>Full SV link:</strong>
|
||
<a href="https://www.ncbi.nlm.nih.gov/projects/sviewer/?id=nc_000001.9&tracks=%5bkey:sequence_track%5d%5bkey:SNP_track%5d%5bkey:gene_model_track,annots:Unnamed%5d%5bkey:dbvar_track,name:dbvar_track1,annots:NA000001999.1%7CNA000002000.1,Rendering:Default%5d%5bkey:dbvar_track,name:dbvar_track2,annots:NA000002001.1,Rendering:SingleLine%5d">http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=nc_000001.9&tracks=%5bkey:sequence_track%5d%5bkey:SNP_track%5d%5bkey:gene_model_track,annots:Unnamed%5d%5bkey:dbvar_track,name:dbvar_track1,annots:NA000001999.1%7CNA000002000.1,Rendering:Default%5d%5bkey:dbvar_track,name:dbvar_track2,annots:NA000002001.1,Rendering:SingleLine%5d</a></p>
|
||
</li>
|
||
<li>
|
||
<p>show tracks with comments specified
|
||
<strong>“track” parameter:</strong></p>
|
||
<p>tracks=[key:gene_model_track,comments:comment%201|28000|comment%202|48000]
|
||
[key:alignment_track]
|
||
\ [key:feature_track,subkey:STS,comments:histogram%20comment%201|20000|histogram%20comment%202|35000|histogram%20comment%203|44000]</p>
|
||
<p><strong>Full SV link:</strong>
|
||
<a href="https://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NG_000007&tracks=%5Bkey:gene_model_track,comments:comment%201%7C28000%7Ccomment%202%7C48000%5D%5Bkey:alignment_track%5D%5Bkey:feature_track,subkey:STS,comments:histogram%20comment%201%7C20000%7Chistogram%20comment%202%7C35000%7Chistogram%20comment%203%7C44000">http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=NG_000007&tracks=%5Bkey:gene_model_track,comments:comment%201%7C28000%7Ccomment%202%7C48000%5D%5Bkey:alignment_track%5D%5Bkey:feature_track,subkey:STS,comments:histogram%20comment%201%7C20000%7Chistogram%20comment%202%7C35000%7Chistogram%20comment%203%7C44000</a></p>
|
||
</li>
|
||
<li>
|
||
<p>tracks settings with ‘highlights’ specified <strong>“track” parameter:</strong></p>
|
||
<p>tracks=[key:sequence_track]
|
||
[key:SNP_track]
|
||
[key:gene_model_track,annots:Unnamed]
|
||
[key:dbvar_track,name:dbvar_track1,annots:NA000001999.1,Rendering:Default,highlights:nsv492962|nssv579665]</p>
|
||
<p><strong>Full SV link:</strong>
|
||
<a href="https://www.ncbi.nlm.nih.gov/projects/sviewer/?id=nc_000001.9&tracks=%5Bkey:sequence_track%5D%5Bkey:SNP_track%5D%5Bkey:gene_model_track,annots:Unnamed%5D%5Bkey:dbvar_track,name:dbvar_track1,annots:NA000001999.1,Rendering:Default,highlights:nsv492962%7Cnssv579665%5D">http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=nc_000001.9&tracks=%5Bkey:sequence_track%5D%5Bkey:SNP_track%5D%5Bkey:gene_model_track,annots:Unnamed%5D%5Bkey:dbvar_track,name:dbvar_track1,annots:NA000001999.1,Rendering:Default,highlights:nsv492962%7Cnssv579665%5D</a></p>
|
||
</li>
|
||
<li>
|
||
<p>tracks settings with ‘filter’ specified
|
||
<strong>“track” parameter:</strong></p>
|
||
<p>tracks=[key:sequence_track]
|
||
[key:feature_track,subkey:STS,name:all,display_name:All STSs]
|
||
[key:feature_track,subkey:STS,filter:len between 260 and 650,name:filtered,display_name:filtered STSs]</p>
|
||
<p><strong>Full SV link:</strong>
|
||
<a href="%20%20%20http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=ng_000007&v=6000..10000&tracks=%5bkey:sequence_track%5d%5bkey:feature_track,subkey:STS,name:all,display_name:All%20STSs5d%5bkey:feature_track,subkey:STS,filter:len%20between%20260%20and%20650,name:filtered,display_name:filtered%20STSs%5d%20%20">http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=ng_000007&v=6000..10000&tracks=[key:sequence_track][key:feature_track,subkey:STS,name:all,display_name:All STSs][key:feature_track,subkey:STS,filter:len between 260 and 650,name:filtered,display_name:filtered STSs]</a></p>
|
||
</li>
|
||
<li>
|
||
<p>tracks settings with ‘sort_by specified
|
||
<strong>“track” parameter:</strong></p>
|
||
<p>tracks=[key:feature_track,name:clone,display_name:Clone%20library\:%20CH242%20Assembly\:%20CCF_000003025.5,subkey:clone,category:Clone,subcategory:CLONES,annots:NA000004255.1,Rendering:Default,sort_by:concordancy]</p>
|
||
<p><strong>Full SV link:</strong>
|
||
<a href="https://www.ncbi.nlm.nih.gov/projects/sviewer/?id=nc_010447.4&tracks=%5Bkey:feature_track,name:clone,display_name:Clone%20library\:%20CH242%20Assembly\:%20CCF_000003025.5,subkey:clone,category:Clone,subcategory:CLONES,annots:NA000004255.1,Rendering:Default,sort_by:concordancy%5D&v=632680:3072449">http://www.ncbi.nlm.nih.gov/projects/sviewer/?id=nc_010447.4&tracks=[key:feature_track,name:clone,display_name:Clone%20library\:%20CH242%20Assembly\:%20CCF_000003025.5,subkey:clone,category:Clone,subcategory:CLONES,annots:NA000004255.1,Rendering:Default,sort_by:concordancy]&v=632680:3072449</a></p>
|
||
</li>
|
||
</ol>
|
||
|
||
|
||
<h3 id="bookmark23">Appendix B: Feature Subtype Storage Keys</h3>
|
||
|
||
|
||
<p><table>
|
||
<tbody>
|
||
<tr>
|
||
<th>
|
||
<span class="s4">Index</span>
|
||
</th>
|
||
<th>
|
||
<span class="s4">Subtype Storage Key</span>
|
||
</th>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">1</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">Gene</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">2</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">Org</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">3</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">CDS</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">4</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">Prot</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">5</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">PreProtein</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">6</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">Mat-Peptide AA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">7</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">Sig-Peptide AA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">8</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">Transit-Peptide AA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">9</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">precursor_RNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">10</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">mRNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">11</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">tRNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">12</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">rRNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">13</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">snRNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">14</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">scRNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">15</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">sno_RNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">16</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">misc_RNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">17</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">ncRNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">18</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">tmRNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">19</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">Pub</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">20</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">Seq</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">21</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">import</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">22</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">allele</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">23</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">attenuator</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">24</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">C_region</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">25</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">CAAT_signal</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">26</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">Imp_CDS</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">27</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">conflict</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">28</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">D-loop</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">29</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">D_segment</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">30</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">enhancer</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">31</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">exon</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">32</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">GC_signal</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">33</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">iDNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">34</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">intron</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">35</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">J_segment</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">36</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">LTR</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">37</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">mat_peptide</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">38</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">misc_binding</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">39</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">misc_difference</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">40</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">misc_feature</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">41</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">misc_recomb</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">42</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">misc_RNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">43</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">misc_signal</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">44</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">misc_structure</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">45</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">modified_base</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">46</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">mutation</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">47</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">N_region</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">48</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">old_sequence</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">49</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">polyA_signal</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">50</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">polyA_site</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">51</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">precursor_RNA</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">52</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">prim_transcript</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">53</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">primer_bind</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">54</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">promoter</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">55</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">protein_bind</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">56</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">RBS</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">57</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">repeat_region</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">58</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">repeat_unit</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">59</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">rep_origin</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">60</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">S_region</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">61</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">satellite</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">62</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">sig_peptide</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">63</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">source</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">64</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">stem_loop</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">65</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">STS</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">66</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">TATA_signal</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">67</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">terminator</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">68</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">transit_peptide</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">69</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">unsure</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">70</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">V_region</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">71</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">V_segment</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">72</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">variation</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">73</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">virion</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">74</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">3'clip</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">75</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">3'UTR</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">76</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">5'clip</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">77</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">5'UTR</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">78</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">-10_signal</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">79</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">-35_signal</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">80</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">gap</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">81</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">operon</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">82</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">oriT</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">83</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">site_ref</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">84</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">mobile_element</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">85</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">region</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">86</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">comment</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">87</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">bond</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">88</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">site</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">89</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">rsite</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">90</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">user</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">91</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">txinit</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">92</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">num</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">93</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">psec_str</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">94</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">non_std_residue</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">95</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">het</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">96</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">biosrc</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">97</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">clone</span>
|
||
</td>
|
||
</tr>
|
||
<tr>
|
||
<td>
|
||
<span class="s4">98</span>
|
||
</td>
|
||
<td>
|
||
<span class="s4">variation</span>
|
||
</td>
|
||
</tr>
|
||
</tbody>
|
||
</table>
|
||
</p>
|
||
|
||
|
||
<hr />
|
||
|
||
|
||
<ol>
|
||
<li><a href="https://www.ncbi.nlm.nih.gov/projects/sviewer/?id=nc_010447.4&tracks" class="s4"></a> <a href="https://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html">http://www.ncbi.nlm.nih.gov/Sitemap/sequenceIDs.html</a></li>
|
||
<li><a href="https://www.ncbi.nlm.nih.gov/books/NBK1058/">http://www.ncbi.nlm.nih.gov/books/NBK1058/</a></li>
|
||
<li><a href="https://eutils.ncbi.nlm.nih.gov/corehtml/query/static/elink_help.html">http://eutils.ncbi.nlm.nih.gov/corehtml/query/static/elink_help.html</a></li>
|
||
<li><a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs">http://blast.ncbi.nlm.nih.gov/Blast.cgi?CMD=Web&PAGE_TYPE=BlastDocs</a></li>
|
||
<li><a href="https://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/rid.html" class="s33">http://www.ncbi.nlm.nih.gov/Class/MLACourse/Modules/BLAST/rid.html</a></li>
|
||
</ol>
|
||
|
||
|
||
<h3 id="bookmark24">Appendix C: Objects/Features tooltips preprocessing</h3>
|
||
|
||
|
||
<p>This feature allows to modify links before they are shown in an Objects/Feature tooltip. It is based on an ability to set a callback function for preprocessing an array of objects describing links coming with the tooltip information.</p>
|
||
|
||
|
||
<p><strong>setTooltipPreprocessor(callback)</strong> - the callback function receives the following two parameters:</p>
|
||
|
||
|
||
<ol>
|
||
<li>Array of link objects:</li>
|
||
</ol>
|
||
|
||
|
||
<p>linksList: [{
|
||
name: string,
|
||
type: string, // 'Extra', 'Basic', 'Download'
|
||
html: string, // may be added by a preprocessor function
|
||
links: [{
|
||
label: string,
|
||
link: string // url
|
||
}, ...]
|
||
},...]</p>
|
||
|
||
|
||
<ol>
|
||
<li>Some extra information about the feature/object:</li>
|
||
</ol>
|
||
|
||
|
||
<p>obj_info: {
|
||
acc: string, //sequence id (accession.ver)
|
||
title: string, // feature/object title
|
||
start_pos: int, // start position
|
||
end_pos: int // end position
|
||
}</p>
|
||
|
||
|
||
<p>If the preprocessing function added <strong>html</strong> property to a <strong>linksList</strong> object Sequence Viewer uses it instead of the array <strong>links</strong> . Removing an object from a <strong>linksList</strong> removes it from the tooltip.</p>
|
||
|
||
|
||
<p>Example (removes each 3rd link from the list):</p>
|
||
|
||
|
||
<pre><code>var app = SeqView.App.findAppByDivId(‘YOUR\_SV\_DIV\_ID’);
|
||
app.setTooltipPreprocessor(function(linksList, obj\_info) {
|
||
for (var i = linksList.length - 1; i >= 0; i--) {
|
||
if (i % 3 == 0) linksList.splice(i, 1);
|
||
}
|
||
</code></pre>
|
||
|
||
|
||
</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>
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<li><a href="/tools/sviewer/extdata/">Adding custom tracks</a></li>
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|
||
<script type="text/javascript" src="/portal/portal3rc.fcgi/rlib/js/InstrumentOmnitureBaseJS/InstrumentNCBIConfigJS/InstrumentNCBIBaseJS/InstrumentPageStarterJS.js?v=1"> </script>
|
||
<script type="text/javascript" src="/portal/portal3rc.fcgi/static/js/hfjs2.js"> </script>
|
||
</div>
|
||
</div>
|
||
<!--/.footer-->
|
||
<p class="last-updated small">Last updated: 2024-02-29T17:18:36Z</p>
|
||
</div>
|
||
<!--/.page-->
|
||
</div>
|
||
<!--/.wrap-->
|
||
<span class="PAFAppResources"></span>
|
||
|
||
|
||
</div><!-- /.twelve_col -->
|
||
</div>
|
||
<!-- /.grid -->
|
||
|
||
|
||
|
||
<!-- usually for JS scripts at page bottom -->
|
||
<span class="pagefixtures"></span>
|
||
|
||
|
||
<!-- CE8B5AF87C7FFCB1_0191SID /projects/staticsites/sviewer/sviewerdoc@1.22 portal105 v4.1.r689238 Tue, Oct 22 2024 16:10:51 -->
|
||
<span id="portal-csrf-token" style="display:none" data-token="CE8B5AF87C7FFCB1_0191SID"></span>
|
||
|
||
|
||
<script type='text/javascript' src='/portal/js/portal.js'></script><script type="text/javascript" src="//static.pubmed.gov/portal/portal3rc.fcgi/4201177/js/3879255/4121861/4187890/2950819.js" snapshot="tools"></script></body>
|
||
</html>
|
||
|