-<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN">\r<html><!-- InstanceBegin template="/Templates/jtemplate.dwt" codeOutsideHTMLIsLocked="false" -->\r<head>\r<!-- InstanceBeginEditable name="doctitle" -->
+<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd">
+<!--
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+-->
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+<head>
<TITLE>Jalview - Applets</TITLE>
-<!-- InstanceEndEditable --> \r<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1"><meta http-equiv="keywords" content="jalview,multiple,sequence,alignment,editor,viewer,java,download,barton group,protein,dna,das,distributed annotation system">\r<!-- InstanceBeginEditable name="head" --><!-- InstanceEndEditable --> \r<style type="text/css">\r<!--\rtd {\r font-family: Geneva, Arial, Helvetica, sans-serif;\r font-size: 12px;\r}\r.plain {\r font-family: Verdana, Arial, Helvetica, sans-serif;\r font-size: 14px;\r text-decoration: none;\r}\r.plain:hover{\r background-color:#000000; color: #F2F2FF;\r}\r \r-->\r</style>\r\r<script language="JavaScript">\rfunction genHref()\r{\rvar s1 = "ml:ljvwr", s2 = "athpai.g", s3 = "ioe@leo ", href="";\rfor(i=0; i<8; i++)\r{href = href + s1.charAt(i) + s2.charAt(i) + s3.charAt(i); }\rwindow.location=href;\r}\rfunction getEventTarget(e)\r{\rif(!e)\re = window.event;\rif(e.target)\rreturn e.target;\rreturn e.srcElement;\r}\r\r</script>\r</head>\r\r<body alink="#000000" vlink="#000000" link="#000000">\r<script type="text/javascript">\rvar gaJsHost = (("https:" == document.location.protocol) ? \r"https://ssl." : "http://www.");\rdocument.write(unescape("%3Cscript src='" + gaJsHost + \r"google-analytics.com/ga.js' type='text/javascript'%3E%3C/script%3E"));\r</script>\r<script type="text/javascript">\rtry{\rvar pageTracker = _gat._getTracker("UA-9060947-1");\rpageTracker._trackPageview();\r} catch(err) {}\r</script>\r<div align="left"> \r <table width="805" height="100" cellpadding="5">\r <tr>\r <td background="../jalview.gif"> <a href="http://www.compbio.dundee.ac.uk" target="NEW"><img src="../uodc_r1_c1.gif" width="143" height="101" border="1"></a></td>\r </tr>\r </table>\r <table width="805" border="0" cellpadding="5" cellspacing="5">\r <tr> \r <td width="183" valign="top" bgcolor="#F2F2FF" border="5"> \r \r <div align="center">\r <table width="182" height="386" border="0" cellpadding="0" cellspacing="0">\r <tr> \r <td align="left" valign="middle"><a href="../index.html" class="plain">Home</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../overview.html" class="plain">Overview</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../download.html" class="plain">Download</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="applets.html" class="plain">Applet \r Version</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="examples.html" class="plain">Screenshots</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../faq.html" class="plain">FAQ</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../documentList.html" class="plain">Documentation</a></td>\r </tr>\r <tr>\r <td align="left" valign="middle" ><a href="../releaseHistory.html" class="plain">Release \r history</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../source/source.html" class="plain">Source \r Code</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../versions.html" class="plain">Development Version</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="../links.html" class="plain">Links</a></td>\r </tr>\r <tr> \r <td align="left" valign="middle"><a href="http://www.jalview.org/mailman/listinfo/jalview-announce" class="plain" target="NEW">News \r Mailing List</a></td>\r </tr>\r <tr>\r <td align="left" valign="middle"><a\r href="http://www.jalview.org/mailman/listinfo/jalview-discuss"\r class="plain" target="NEW">Discussion Mailing List</a><br><br><em>Please send problems<br>and\r bug reports to the discussion list.</em></td>\r </tr>\r <tr></tr>\r <tr>\r <!--<td align="left" valign="middle"><br>\r Please send problems<br>and\r bug reports to:<br><a href="#" onClick="javascript:genHref();"><img src="../help.gif" width="123" height="19" border="0"></a></td>-->\r </tr>\r </table>\r\r </div>\r\r <div align="center"> <a href="http://www.bbsrc.ac.uk/" target="NEW"><br>\r <img src="../bbsrc-new.gif" width="179" height="64" border="1"></a> \r </div>\r </td>\r <td valign="top" width="587" bgcolor="#F2F2FF"><!-- InstanceBeginEditable name="Contents" -->
- <p>Jalview comes in two distinct flavours.<br>
- <br>
- The main application allows connection to multiple web services provided
- at the University of Dundee as well as a host of additional useful features
- such as printing, making images from your alignment and annotating your
- alignment. You need to download and install this software.</p>
- <p>The applet version runs in web browsers and is a useful interactive
- display for precalculated alignments, features and annotations files.
- It does not have the full functionality of the main application, such
- as making images, saving files, running web service jobs due to security
- restrictions imposed on applets.</p>
- <p align="left">For more information on how to use the applet in your
- website, see <a href="appletParameters.html"><strong>full list of applet
- parameters.</strong></a></p>
- <p> Pressing one of the buttons below will load up JalviewLite, a cut down version
- of Jalview, which runs within your web browser. </p>
- <H4 align="center"> Ferredoxins, chloroplast precursor related UniRef50
- cluster<br>
- (15 sequences x 150 residues)</H4>
- <div align="center"> </div>
- <div align="center">
- <table width="300" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td><table width="300" border="0" cellspacing="0" cellpadding="0">
- <tr>
- <td width="100"> <applet code="jalview.bin.JalviewLite"
- width="140" height="35"
- archive="jalviewApplet.jar">
- <param name="file" value="uniref50.fa">
- <param name="treeFile" value="ferredoxin.nw">
- <param name="userDefinedColour" value="C=yellow; R,K,H=FF5555; D,E=5555FF">
- <param name="showFullId" value="false">
- <param name="RGB" value="F2F2FF">
- <param name="linkLabel_1" value="SRS">
- <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
- <param name="linkLabel_2" value="Uniprot">
- <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
- <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
- </applet></td>
- <td width="165">User Defined Colours, loads an associated Newick
- format tree file</td>
- </tr>
- </table></td>
- </tr>
- </table>
- <p> </p>
- <table width="300" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td><table width="300" border="0" cellspacing="0" cellpadding="0">
- <tr>
- <td width="100"> <applet code="jalview.bin.JalviewLite"
- width="140" height="35"
- archive="jalviewApplet.jar">
- <param name="file" value="uniref50.fa">
- <param name="features" value="exampleFeatures.txt">
- <param name="showFeatureSettings" value="true">
- <param name="wrap" value="true">
- <param name="showAnnotation" value="false">
- <param name="windowHeight" value="500">
- <param name="windowWidth" value="650">
- <param name="showFullId" value="false">
- <param name="RGB" value="F2F2FF">
- <param name="linkLabel_1" value="SRS">
- <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
- <param name="linkLabel_2" value="Uniprot">
- <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
- <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
- </applet> </td>
- <td width="165">Displays a features file on the alignment</td>
- </tr>
- </table></td>
- </tr>
- </table>
- <p> </p>
- <table width="300" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td><table width="300" border="0" cellspacing="0" cellpadding="0">
- <tr>
- <td width="100"> <applet code="jalview.bin.JalviewLite"
- width="140" height="35"
- archive="jalviewApplet.jar,JmolApplet-12.1.13.jar">
- <param name="file" value="uniref50.fa">\r <!-- <param name="debug" value="true">
- -->\r <param name="defaultColour" value="Strand Propensity">
- <param name="wrap" value="true">
- <param name="showAnnotation" value="false">
- <param name="windowHeight" value="500">
- <param name="windowWidth" value="650">
- <param name="showFullId" value="false">
- <param name="RGB" value="F2F2FF">
- <param name="linkLabel_1" value="SRS">
- <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
- <param name="linkLabel_2" value="Uniprot">
- <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
- <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
- <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
- </applet> </td>
- <td width="165">Associates PDB file 1GAQ with sequence FER1_MAIZE</td>
- </tr>
- </table></td>
- </tr>
- </table>
- <p> </p>
- <table width="300" border="1" cellspacing="0" cellpadding="0">
- <tr>
- <td><table width="300" border="0" cellspacing="0" cellpadding="0">
- <tr>
- <td width="100"> <applet code="jalview.bin.JalviewLite"
- width="140" height="35"
- archive="jalviewApplet.jar">
- <param name="file" value="jpred_msa.fasta">
- <param name="jnetfile" value="jpred_msa.seq.concise">
- <param name="defaultColour" value="Clustal">
- <param name="showAnnotation" value="true">
- <param name="windowHeight" value="515">
- <param name="windowWidth" value="650">
- <param name="showConservation" value="false">
- <param name="showQuality" value="false">
- <param name="showConsensus" value="false">
- <param name="showFullId" value="false">
- <param name="RGB" value="F2F2FF">
- <param name="linkLabel_1" value="SRS">
- <param name="linkUrl_1" value="http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2">
- <param name="linkLabel_2" value="Uniprot">
- <param name="linkUrl_2" value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
- <param name="APPLICATION_URL" value="http://www.jalview.org/services/launchApp">
- </applet> </td>
- <td width="165">Displays a Multiple Sequence Alignment Based
- JNet Prediction for a Sequence</td>
- </tr>
- </table></td>
- </tr>
- </table>\r
- </div>\r <p> </p>\r <p>For more JalviewLite examples, follow the links below.\r <ul>\r <li><a href="embedded.html">JalviewLite embedded in the web page</a></li>\r <li><a href="formComplete.html">use Javascript to control and get data from JalviewLite</a></li>\r <li><a href="linkedapplets_ng.html">use Javascript to make two jalviewLite instances talk to each other</a></li>\r <li><a href="embeddedWJmol.html">configure JalviewLite to talk to a Jmol applet on the page.</a></li>\r </ul>
- <!-- InstanceEndEditable --></td>\r </tr>\r </table>\r</div>\r</body>\r<!-- InstanceEnd --></html>\r
\ No newline at end of file
+<meta http-equiv="Content-Type" content="text/html; charset=UTF-8" />
+
+ <link href="css/reset.css" rel="stylesheet" type="text/css" />
+ <link href="css/style.css" rel="stylesheet" type="text/css" />
+
+ <!--[if IE 6]>
+ <link rel="stylesheet" type="text/css" href="css/ie6.css" />
+<![endif]-->
+
+<!--[if IE 7]>
+ <link rel="stylesheet" type="text/css" href="css/ie7.css" />
+<![endif]-->
+
+<!-- dd menu -->
+<script type="text/javascript">
+<!--
+var timeout = 500;
+var closetimer = 0;
+var ddmenuitem = 0;
+
+// open hidden layer
+function mopen(id)
+{
+ // cancel close timer
+ mcancelclosetime();
+
+ // close old layer
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+
+ // get new layer and show it
+ ddmenuitem = document.getElementById(id);
+ ddmenuitem.style.visibility = 'visible';
+
+}
+// close showed layer
+function mclose()
+{
+ if(ddmenuitem) ddmenuitem.style.visibility = 'hidden';
+}
+
+// go close timer
+function mclosetime()
+{
+ closetimer = window.setTimeout(mclose, timeout);
+}
+
+// cancel close timer
+function mcancelclosetime()
+{
+ if(closetimer)
+ {
+ window.clearTimeout(closetimer);
+ closetimer = null;
+ }
+}
+
+// close layer when click-out
+document.onclick = mclose;
+// -->
+</script>
+<script>
+<!--//--><![CDATA[//><!--
+var _gaq = _gaq || [];_gaq.push(["_setAccount", "UA-9060947-1"]);_gaq.push(["_trackPageview"]);(function() {var ga = document.createElement("script");ga.type = "text/javascript";ga.async = true;ga.src = ("https:" == document.location.protocol ? "https://ssl" : "http://www") + ".google-analytics.com/ga.js";var s = document.getElementsByTagName("script")[0];s.parentNode.insertBefore(ga, s);})();
+//--><!]]>
+</script>
+</head>
+
+
+<body>
+
+
+<div id="header">
+<div id="logo"><a href="http://www.jalview.org" title="Home"></a></div>
+<ul id="buttons">
+<li id="applet"><a href="applets.html" title="applet"></a></li>
+<li id="desktop"><a href="../webstart/jalview.jnlp" title="desktop"></a></li>
+</ul>
+</div>
+
+
+<div id ="nav">
+<div id="navInner">
+
+<ul id="sddm">
+ <li><a href="http://www.jalview.org">Home</a></li>
+ <li><a href="http://www.jalview.org/about" onmouseover="mopen('m1')" onmouseout="mclosetime()">About</a>
+ <div id="m1" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/about/documentation">Documentation</a>
+ <a href="http://www.jalview.org/about/citation">Publications</a>
+ <a href="http://www.jalview.org/about/credits">Credits</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/faq">FAQ</a></li>
+ <li><a href="http://www.jalview.org/community" onmouseover="mopen('m3')" onmouseout="mclosetime()" class="community">Community</a>
+ <div id="m3" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-announce">News Mailing List</a>
+ <a href="http://www.jalview.org/mailman/listinfo/jalview-discuss">Discussion Mailing List</a>
+ <a href="http://www.jalview.org/community/links">Links</a>
+ <a href="http://www.jalview.org/community/community-news">Community News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/development" onmouseover="mopen('m4')" onmouseout="mclosetime()" class="development">Development</a>
+ <div id="m4" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/development/release-history">Release History</a>
+ <a href="http://issues.jalview.org">Jalview Bug Tracker</a>
+ <a href="http://source.jalview.org/gitweb/">Jalview Git Web</a>
+ <a href="http://www.jalview.org/development/development-news">Development News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/training" onmouseover="mopen('m5')" onmouseout="mclosetime()" class="training">Training</a>
+ <div id="m5" onmouseover="mcancelclosetime()" onmouseout="mclosetime()">
+ <a href="http://www.jalview.org/training/training-courses">Training Courses</a>
+ <a href="http://www.jalview.org/training/training-news">Training News</a>
+ </div>
+ </li>
+ <li><a href="http://www.jalview.org/download" class="download-right">Download</a></li>
+</ul>
+<div style="clear:both"></div>
+</div>
+
+</div>
+
+
+ <div id="pageWrap">
+
+ <div id="sideNav">
+ <ul>
+ <li class="jvlite-nav-title"><a href="applets.html">JalviewLite
+ Examples</a></li>
+ <li><a href="appletParameters.html">Applet Parameters</a></li>
+ <li><a href="jalviewLiteJs.html">Javascript API</a></li>
+ <li><a href="formComplete.html">in-page API demo</a></li>
+ <li><a href="linkedapplets_ng.html">Two JalviewLites demo</a></li>
+ <li><a href="embeddedWJmol.html">Jalview and Jmol demo</a></li>
+ </ul>
+ </div>
+
+ <div id="content" class="content">
+ <p>JalviewLite is a web based version of Jalview, which runs as a
+ Java applet in or on a web page. It's one of the easiest ways of
+ providing an interactive display for precalculated alignments,
+ features and annotations files. It lacks some functionality
+ available in the Jalview Desktop, however, such as making images,
+ saving files, and running web service jobs. This is mostly due to
+ security restrictions imposed on applets.</p>
+ <p align="left">
+ Try out JalviewLite by pressing one of the buttons below. For more information on how to use the applet in your website, see the <a
+ href="appletParameters.html"><strong>applet parameters</strong></a> and other documentation in the links to the left.</p>
+ <div align="center">
+ <p>
+ <h2>Ferredoxins, chloroplast precursor related UniRef50
+ cluster</h2>
+ <br /> (15 sequences x 150 residues)
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+ <param name="file" value="uniref50.fa">
+ <param name="treeFile" value="ferredoxin.nw">
+ <param name="userDefinedColour"
+ value="C=yellow; R,K,H=FF5555; D,E=5555FF">
+ <param name="showFullId" value="false">
+ <param name="sortByTree" value="True">
+ <param name="showSequenceLogo" value="true">
+ <param name="showGroupConsensus" value="true">
+ <param name="linkLabel_1" value="Uniprot">
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="Expasy">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp">
+ </applet></td>
+ <td valign="center">User Defined Colours, loads an associated
+ Newick format tree file which is used to sort the alignment, and
+ group consensus and sequence logos are shown below the alignment.</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+ <param name="file" value="uniref50.fa">
+ <param name="features" value="exampleFeatures.txt">
+ <param name="showFeatureSettings" value="true">
+ <param name="wrap" value="true">
+ <param name="showAnnotation" value="false">
+ <param name="windowHeight" value="500">
+ <param name="windowWidth" value="650">
+ <param name="showFullId" value="false">
+ <param name="linkLabel_1" value="Uniprot">
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="Expasy">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp">
+ </applet></td>
+ <td valign="center">Displays a features file on the alignment</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar,JmolApplet-12.2.4.jar">
+<param name="permissions" value="sandbox">
+ <param name="file" value="uniref50.fa">
+ <!-- <param name="debug" value="true">
+ -->
+ <param name="defaultColour" value="Strand Propensity">
+ <param name="wrap" value="true">
+ <param name="showAnnotation" value="false">
+ <param name="windowHeight" value="500">
+ <param name="windowWidth" value="650">
+ <param name="showFullId" value="false">
+ <param name="linkLabel_1" value="Uniprot">
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="Expasy">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp">
+ <param name="PDBfile" value="1gaq.txt FER1_MAIZE">
+ </applet></td>
+ <td valign="center">Associates PDB file 1GAQ with sequence
+ FER1_MAIZE</td>
+ </tr>
+ <tr>
+ <td width="10%" valign="middle"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+ <param name="file" value="jpred_msa.fasta">
+ <param name="jnetfile" value="jpred_msa.seq.concise">
+ <param name="defaultColour" value="Clustal">
+ <param name="showAnnotation" value="true">
+ <param name="windowHeight" value="515">
+ <param name="windowWidth" value="650">
+ <param name="showConservation" value="false">
+ <param name="showQuality" value="false">
+ <param name="showConsensus" value="false">
+ <param name="showFullId" value="false">
+ <param name="linkLabel_1" value="Uniprot">
+ <param name="linkUrl_1"
+ value="http://www.uniprot.org/uniprot/$SEQUENCE_ID$">
+ <param name="linkLabel_2" value="Expasy">
+ <param name="linkUrl_2"
+ value="http://us.expasy.org/cgi-bin/niceprot.pl?$SEQUENCE_ID$">
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp">
+ </applet></td>
+ <td valign="center">Displays a Multiple Sequence Alignment
+ Based JNet Prediction for a Sequence</td>
+ </tr>
+ </table>
+ <p>
+ <h2>RF00031 RFAM Alignment with per sequence secondary
+ structure</h2>
+ </p>
+ <table width="90%">
+ <tr>
+ <td width="10%" valign="center"><applet
+ code="jalview.bin.JalviewLite" width="140" height="35"
+ archive="jalviewApplet.jar">
+<param name="permissions" value="sandbox">
+ <param name="file" value="RF00031_folded.stk">
+ <param name="defaultColour" value="Purine/Pyrimidine">
+ <param name="showAnnotation" value="true">
+ <param name="windowHeight" value="515">
+ <param name="windowWidth" value="650">
+ <param name="showConservation" value="false">
+ <param name="showQuality" value="false">
+ <param name="showConsensus" value="true">
+ <param name="showFullId" value="false">
+ <param name="APPLICATION_URL"
+ value="http://www.jalview.org/services/launchApp">
+ </applet></td>
+ <td valign="center">Displays an RFAM RNA fold family with
+ secondary structure annotation</td>
+ </tr>
+ </table>
+ </div>
+ </div>
+ </div>
+
+<div id ="footer">
+<div id="innerFooter">
+<div id="copyright"><p>Published under <a href="http://creativecommons.org/licenses/by-sa/3.0/">CC-SA 3.0</a></p></div>
+<div id="cite">
+<p>
+If you use Jalview in your work, please cite this publication:
+</p>
+<br />
+<p>
+Waterhouse, A.M., Procter, J.B., Martin, D.M.A, Clamp, M. and Barton, G. J. (2009)
+"Jalview Version 2 - a multiple sequence alignment editor and analysis workbench"
+Bioinformatics 25 (9) 1189-1191 <a href="http://dx.doi.org/10.1093/bioinformatics/btp033">doi: 10.1093/bioinformatics/btp033</a>
+</p>
+</div>
+</div>
+</div>
+</body>
+</html>
+