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index.php
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<?php require_once("config.php"); ?>
<html>
<head>
<meta charset="utf-8" />
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<title>ConVarT</title>
<meta name="description" content="ConVarT (Conserved clinical Variation visualization Tool) is a specialized tool that facilitates consistent and rapid visualization of cross-species conservation of human genetic variants and post-translational modifications (PTMs) with minimal effort.">
<meta name="title" content="ConVarT">
<meta name="keywords" content="ConVarT"/>
<meta name="author" content="ConVarT">
<meta name="copyright" content="ConVarT">
<link rel="icon" href="files/img/convart_black.png">
<link href="https://fonts.googleapis.com/icon?family=Material+Icons" rel="stylesheet">
<link type="text/css" rel="stylesheet" href="files/css/style.css" media="screen"/>
<link type="text/css" rel="stylesheet" href="files/css/CurrentProject.css?id=<?= rand(); ?>" media="screen,projection"/>
<meta name="viewport" content="width=device-width, initial-scale=1">
<script src="https://code.jquery.com/jquery-3.3.1.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<script src='https://www.google.com/recaptcha/api.js' async defer></script>
</head>
<body id="CurrentProjectHomePage">
<!-- Header -->
<ul id="info-menu" class="dropdown-content">
<li><a href="pages/About.php">About</a></li>
<li><a href="pages/Help.php">Help</a></li>
<li><a href="pages/Faq.php">FAQs</a></li>
<li><a href="pages/Citation.php">How to cite ConVarT</a></li>
<li><a href="pages/Database.php">Database Schema</a></li>
<li><a onclick="Materialize.toast('Coming Soon!', 4000)">API</a></li>
<li><a href="pages/Contact.php">Contact</a></li>
<li><a href="pages/Terms.php">Terms</a></li>
</ul>
<ul id="explore-menu" class="dropdown-content">
<li><a href="pages/DiseaseStatistics.php">Disease Statistics</a></li>
<li><a href="pages/ClinVarStatistics.php">ClinVar Statistics</a></li>
<li><a href="pages/PTM_gnomAD_COSMIC.php">PTM, gnomAD and COSMIC Statistics</a></li>
<li><a href="pages/ClinVarGeneHomology.php">ClinVar and Gene Homology</a></li>
<li><a href="pages/Downloads.php">Download Data</a></li>
</ul>
<div class="navbar-fixed"><nav>
<div class="nav-wrapper sitemenu">
<a href="http://convart.org" class="brand-logo sitelogo"><img src="files/img/convart.png" class="sitelogoimg"></a>
<a href="#" data-activates="mobile-demo" class="button-collapse white-text"><i class="mobilbuton material-icons">menu</i></a>
<ul class="right hide-on-med-and-down menulinks">
<li><a href="index.php">Home</a></li>
<li><a class="dropdown-button" href="#!" data-activates="info-menu">Info<i class="material-icons right">arrow_drop_down</i></a></li>
<li><a class="dropdown-button" href="#!" data-activates="explore-menu">Explore<i class="material-icons right">arrow_drop_down</i></a></li>
<li><a href="pages/Submit.php">Submit</a></li>
</ul>
<ul class="side-nav" id="mobile-demo">
<li><a href="pages/About.php">About</a></li>
<li><a href="pages/Help.php">Help</a></li>
<li><a href="pages/Faq.php">FAQs</a></li>
<li><a href="pages/Citation.php">How to cite ConVarT</a></li>
<li><a href="pages/Experiments.php">Experimental Validation</a></li>
<li><a href="pages/Database.php">Database Schema</a></li>
<li><a onclick="Materialize.toast('Coming Soon!', 4000)">API</a></li>
<li><a href="pages/Contact.php">Contact</a></li>
<li><a href="pages/Terms.php">Terms</a></li>
<li><a href="pages/DiseaseStatistics.php">Disease Statistics</a></li>
<li><a href="pages/ClinVarStatistics.php">ClinVar Statistics</a></li>
<li><a href="pages/PTM_gnomAD_COSMIC.php">PTM, gnomAD and COSMIC Statistics</a></li>
<li><a href="pages/ClinVarGeneHomology.php">ClinVar and Gene Homology</a></li>
<li><a href="pages/Downloads.php">Download Data</a></li>
<li><a href="pages/Submit.php">Submit</a></li>
</ul>
</div>
</nav></div> <!-- end of header -->
<!-- ConVarT -->
<div class="container pageBox home">
<div class="row"><br>
<div class="col s12 l12 m12"><img src="./files/img/convart.png" alt="Current Project" class="homePageLogo center"></div>
</div>
<div class="row">
<ul class="tabs searching-tabs">
<li class="tab searching-tab col s0 m0 l2"></li>
<li class="tab searching-tab col s4 m4 l2"><a class="active" href="#spemud-search"><b>S</b>pe<b>M</b>u<b>D</b></a></li>
<li class="tab searching-tab col s4 m4 l3"><a href="#gene-search">Gene Search</a></li>
<li class="tab searching-tab col s4 m4 l3"><a href="#disease-search">Disease Search</a></li>
<li class="tab searching-tab col s4 m4 l2"></li>
</ul>
</div>
<!-- Spemud search -->
<div id="spemud-search" class="col s12">
<!-- <br><p class="center-align"><b>Select your proteins and visualize them with variants:</b></p> -->
<form action="<?= $GLOBALS['base_url']; ?>search" method="get" class="spemudForm" autocomplete="off">
<div class="row"><br>
<div class="col s12 m12 l3"></div>
<div class="col s12 m12 l6">
<a href="#findHumanHomolog" class="modal-trigger tooltipped btn waves-effect waves-light waves-white seqSearchButton" style="width: 100% !important;" data-position="right"
data-tooltip="Find human ortolog of the gene of your interest"><i class="material-icons">list</i> Find the human homologs of a gene </a>
<h4 style="text-align:center; margin-top:0.8em; margin-bottom:0.5em; padding: 0">OR</h4>
<input name="spemud" id="spemud" type="text" class="searchbox" placeholder="Type a human gene name or protein ID" required>
<p class="center-align">Example: <i>HARS</i>, NP_000010</p>
</div>
<div class="col s12 m12 l4"></div>
</div>
<div class="row"><br>
<div class="col s12 m12 l12"><center>
<button class="btn waves-effect waves-light waves-white sb seqSearchButton" type="submit"><i class="material-icons">search</i>ANALYSE</button>
</center></div>
</div>
</form>
</div>
<!-- gene search -->
<div id="gene-search" class="col s12">
<form action="<?= $GLOBALS['base_url']; ?>search" method="get" class="mainForm" autocomplete="off">
<div class="row">
<div class="col s1 m1 l3"></div>
<div class="col s9 m9 l5">
<input name="searchText" id="searchTerm" type="text" class="searchbox" placeholder="Search a gene, GeneID, Ensembl ID or protein number" required>
</div>
<div class="col s1 m1 l1"><button style="float:right;" class="btn waves-effect waves-light waves-white sb" type="submit"><i class="material-icons">search</i></button></div>
<div class="col s1 m1 l2"></div>
</div>
<div class="row">
<div class="col s0 m0 l3"> </div>
<div class="col s12 m12 l6 center-align">
<a class="home_link" href="<?= $GLOBALS['base_url']; ?>msa?id=NP_006504.2">HGNC:10537</a> ,
<a class="home_link" href="<?= $GLOBALS['base_url']; ?>msa?id=NP_002100">rs191391414</a> , <!-- -->
<a class="home_link" href="<?= $GLOBALS['base_url']; ?>msa?id=NP_001004252">Farslb</a>,
<a class="home_link" href="<?= $GLOBALS['base_url']; ?>msa?id=NP_032240">MGI:108087</a>,
<a class="home_link" href="<?= $GLOBALS['base_url']; ?>msa?id=NP_001007769">ZDB-GENE-021206-2</a>,
<a class="home_link" href="<?= $GLOBALS['base_url']; ?>msa?id=NP_524366">FBgn0026634</a>,
<a class="home_link" href="<?= $GLOBALS['base_url']; ?>msa?id=NP_001005694.1">XB-GENE-1000989</a>,
<a class="home_link" href="<?= $GLOBALS['base_url']; ?>msa?id=NP_499796.2">WBGene00003373</a>
<a href="#identifier_types_help" class="modal-trigger tooltipped" data-position="right" data-delay="10" data-tooltip="Explore the catalog of the gene identifiers you can search"><i class="material-icons white-text text-darken-1">help</i></a>
</p>
</div>
<div class="col s0 m0 l3"> </div>
</div>
</form>
<!-- Sequence Search in gene search -->
<h4 class="center-align" style="text-align:center; margin-top:0.8em; margin-bottom:0.5em; padding: 0">OR</h4>
<div class="row">
<form action="<?= $GLOBALS['base_url']; ?>blast_query.php" method="post" name="seqSearch" autocomplete="off">
<div class="col l12 m12 s12"><center>
<textarea id="sequenceArea" name="sequence" class="materialize-textarea sequenceArea"
placeholder=">NP_592921.1 putative AP-2 adaptor complex subunit Apm4 [S. pombe]
MISGLFIFNLKGDTLICKTFRHDLKKSVTEIFRVAILTNTDYRHPIVSIGSSTYIYTKHEDLYVVAITKGNPNVMIVLEFLESLIQDLTHYFGKLNENTVKDNVSFIFELLDEMIDYGIIQTTEPDALARSVSITAVKKKGNALSLKRSHSSQLAHTTSSEIPGSVPWRRAGIKYRKNSIYIDIVERMNLLISSTGNVLRSDVSGVVKMRAMLSGMPECQFGLNDKLDFKLKQSESKSKSNNSRNPSSVNGGFVILEDCQFHQCVRLPEFENEHRITFIPPDGEVELMSYRSHENINIPFRIVPIVEQLSKQKIIYRISIRADYPHKLSSSLNFRIPVPTNVVKANPRVNRGKAGYEPSENIINWKIPRFLGETELIFYAEVELSNTTNQQIWAKPPISLDFNILMFTSSGLHVQYLRVSEPSNSKYKSIKWVRYSTRAGTCEIRI" required></textarea>
<div class="g-recaptcha" data-sitekey="6LdZMaMUAAAAAAJdY4SpK0vOHHFnf-Ff5iVOp1K4"></div>
<div class="row"><button class="btn waves-effect waves-light waves-white sb seqSearchButton" type="submit"><i class="material-icons">search</i>SEARCH</button></center></div>
</form>
<center><a class="twitter-share-button" href="https://twitter.com/intent/tweet" data-size="large" data-text="Here is ConVarT (Conserved clinical Variation visualization Tool)! Check it out on "
data-url="http://www.convart.org/" data-hashtags=" ConVarT,ModelOrganismCommunity" data-show-count="true" data-via="CiliopathyLab" data-lang="en"> Tweet </a></center>
<!--<div class="chip"> Our work will be presented at <a href="eshg2019">#ESHG2019</a> on 17th June. <i class="close material-icons">close</i> </div>
<a href="<?= $GLOBALS['base_url']; ?>seqSearch.php" class="btn waves-effect waves-light waves-blue white blue-text center seqSearchButtonHome"><i class="material-icons left">format_align_center</i> Search with protein sequence</a><br> -->
</div>
</div>
<!-- disease search -->
<div id="disease-search" class="col s12">
<div class="row">
<form action="<?= $GLOBALS['base_url']; ?>disease" method="get" class="mainForm" autocomplete="off">
<div class="col s1 m1 l3"></div>
<div class="col s9 m9 l5">
<input name="searchText" id="searchTerm" type="text" class="searchbox" placeholder="Search a disease name" required>
<p class="center-align"><a class="home_link" href="diseases.php?q=Joubert+Syndrome">Joubert Syndrome</a> , <a class="home_link" href="diseases.php?q=Alzheimer">Alzheimer</a> , <a class="home_link" href="diseases.php?q=Acute+Myeloid+Leukemia">Acute Myeloid Leukemia</a></p>
</div>
<div class="col s1 m1 l1"><button class="btn waves-effect waves-light waves-white sb" type="submit"><i class="material-icons">search</i></button></div>
<div class="col s1 m1 l3"></div>
</form>
</div>
</div>
</div>
</div> <!-- ConVarT -->
<!-- Human Homolog Modal -->
<div id="findHumanHomolog" class="modal modal-fixed-footer">
<div class="row">
<div class="modal-content">
<h4>Find human homolog of your gene</h4>
<iframe src="spemud_helper_flow.php" id="spemud-helper-flow" frameborder="0" width="100%" height="500"></iframe>
</div>
<div class="modal-footer">
<a href="#!" class="modal-action modal-close waves-effect waves-green btn-flat blue white-text">Close</a>
</div>
</div>
</div>
<!-- Modal Structure -->
<div id="identifier_types_help" class="modal modal-fixed-footer">
<div class="modal-content">
<h4>List of the Searching Identifiers</h4>
<p>
<table class="special_table">
<th>Identifier Name</th>
<th>Description</th>
<tr>
<td>NCBI Gene ID</td>
<td>NCBI Gene ID (e.g. 6301)</td>
</tr>
<tr>
<td>Gene Symbol</td>
<td>Current Gene Symbol (e.g. <i>SARS</i>, <i>sars-1</i>)</td>
</tr>
<tr>
<td>Gene Synonmys</td>
<td>Previous Gene Symbols (e.g. <i>SERRS</i>)</td>
</tr>
<tr>
<td>HGNC</td>
<td>HUGO Gene Nomenclature Committee (e.g. HGNC:10537)</td>
</tr>
<tr>
<td>ENSEMBL GENE ID</td>
<td>ENSEMBL Gene IDs for any specie in our database <br> (e.g. ENSG00000031698, ENSMUSG00000068739, ENSRNOG00000020255,<br> ENSDARG00000008237, ENSPTRG00000001043, ENSMMUG00000021837)</td>
</tr>
<tr>
<td>RS Number</td>
<td>Reference SNP ID (e.g. rs191391414)</td>
</tr>
<tr>
<td>Protein Acc. Number</td>
<td>NCBI Protein Accession Numbers (e.g. NP_006504.2, XP_006233198.1)</td>
</tr>
<tr>
<td>MGI ID</td>
<td>MGI-Mouse Genome Informatics (e.g. MGI:102809)</td>
</tr>
<tr>
<td>ZFIN ID</td>
<td>ZFIN The Zebrafish Information Network (e.g. ZDB-GENE-040831-1)</td>
</tr>
<tr>
<td>FB Gene ID</td>
<td>FlyBase Gene ID (e.g. FBgn0031497)</td>
</tr>
<tr>
<td>WB Gene ID</td>
<td>WormBase Gene ID(e.g. WBGene00005663)</td>
</tr>
</table>
</p>
</div>
<div class="modal-footer">
<a href="#!" class="modal-action modal-close waves-effect waves-green btn-flat blue white-text">Agree</a>
</div>
</div>
<script src="https://code.jquery.com/jquery-3.3.1.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script>
<script src="files/js/js.js"></script>
<script src="files/js/CurrentProject.js"></script>
<script type="text/javascript">
$('.mainForm').submit(function(e) {
e.preventDefault();
window.location = $(this).prop('action')+'?q='+$(this).find('input[type=text]').val() ;
return false;
});
</script>
<script>
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return t;
}(document, "script", "twitter-wjs"));
</script>
<script>
$(document).ready(function () {
url = window.location.href;
key = url.split("?err=")[1]
if (key == "page_error") {
Materialize.toast("You used incorrect adress or link. You are redirected to home page.", 5500, "rounded");
}
if (key == "verify_robot") {
Materialize.toast("Please verify you are not robot!", 5500, "rounded");
}
if (key == "maintenance") {
window.location.href = "http://convart.org/503.html";
}
});
</script>
</body>
</html>