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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta http-equiv="X-UA-Compatible" content="IE=edge">
<meta name="viewport" content="width=device-width, initial-scale=1">
<meta name="author" content="Hashem A. Shihab">
<meta name="description" content="a method for visualizing functional predictions of single nucleotide variants across the human genome.">
<title>Genome Tolerance Browser</title>
<link href="./css/bootstrap.min.css" rel="stylesheet">
<link href="./css/font-awesome.min.css" rel="stylesheet">
<style>
// Sidebar adapted from http://www.bootply.com/
body {
padding-top: 50px;
}
#masthead {
min-height: 250px;
text-align: justify;
}
#masthead h1 {
font-size: 30px;
line-height: 1;
padding-top: 20px;
}
#masthead .well {
margin-top: 8%;
}
@media screen and (min-width: 768px) {
#masthead h1 {
font-size: 50px;
}
}
.navbar-bright {
background-color: #111155;
color: #fff;
}
.affix-top,
.affix {
position: static;
}
@media (min-width: 979px) {
#sidebar.affix-top {
position: static;
margin-top: 30px;
width: 228px;
}
#sidebar.affix {
position: fixed;
top: 70px;
width: 228px;
}
}
#sidebar li.active {
border: 0 #eee solid;
border-right-width: 5px;
}
</style>
<!--[if lt IE 9]>
<script src="https://oss.maxcdn.com/html5shiv/3.7.2/html5shiv.min.js"></script>
<script src="https://oss.maxcdn.com/respond/1.4.2/respond.min.js"></script>
<![endif]-->
</head>
<body>
<nav class="navbar navbar-inverse navbar-fixed-top">
<div class="container">
<div class="navbar-header pull-left">
<a class="navbar-brand" href="./index.htm">Genome Tolerance Browser</a>
</div>
<div class="navbar-header pull-right">
<a class="navbar-brand" href="./faq.htm">Help</a>
</div>
</div>
</nav>
<br />
<br />
<br />
<br />
<div id="masthead">
<div class="container">
<div class="row">
<!-- Sidebar -->
<div class="col-md-3" id="leftCol">
<ul class="nav nav-stacked" id="sidebar">
<li><a href="#about">About</a></li>
<li><a href="#methods">Available Methods</a></li>
<li><a href="#tracks">Adding & Amending Tracks</a></li>
<li><a href="#export">Exporting Images</a></li>
<li><a href="#response">Unresponsive Browser</a></li>
<li><a href="#contact">Contact Us</a></li>
</ul>
</div>
<!-- Content -->
<div class="col-md-9">
<h2 id="about">About</h2>
<hr>
<p>
The Genome Tolerance Browser is an online genome browser for visualizing the predicted tolerance of the human genome.
For each position across the genome, we compiled normalized functional predictions from numerous non-synonymous computational predictions algorithms, such as SIFT and PolyPhen,
genome-wide computational prediction algortihms, such as FATHMM-MKL and CADD,
and cancer-specific prediction algorithms, such as FATHMM-Cancer and TransFIC.
The interactive browser can be used to facilitate the rapid identification of predicted intolerant regions across the genome and can also be used to visualize the concordance & subtle differences
between multiple prediction algorithms.
<br />
<br />
<b>If you have found this resource useful, please cite our publication:</b>
<br />
<br />
<ul>
<li> Shihab HA, Rogers MF, Campbell C, Gaunt TR. 2015. GTB – An Online Genome Tolerance Browser. (Submitted)</li>
</ul>
</p>
<br />
<h2 id="methods">Available Methods</h2>
<hr>
<table class="table table-striped">
<thead>
<tr>
<th width="20%">id</th>
<th>Method/Description</th>
<th width="10%">Download</th>
</tr>
</thead>
<tbody>
<tr>
<td colspan=3>
<h3>Non-Synonymous/Coding Prediction Algorithms</h3>
</td>
</tr>
<tr>
<td>SIFT</td>
<td>SIFT</td>
<td><a href="./tracks/SIFT.bw">bigWig</a></td>
</tr>
<tr>
<td>PPH2_HVAR</td>
<td>PolyPhen-2 (HumVar)</td>
<td><a href="./tracks/PPH2_HVAR.bw">bigWig</a></td>
</tr>
<tr>
<td>PPH2_HDIV</td>
<td>PolyPhen-2 (HumDiv)</td>
<td><a href="./tracks/PPH2_HDIV.bw">bigWig</a></td>
</tr>
<tr>
<td>FATHMM_MKLC</td>
<td>FATHMM-MKL (Coding)</td>
<td><a href="./tracks/FATHMM_MKLC.bw">bigWig</a></td>
</tr>
<tr>
<td>FATHMM_U</td>
<td>FATHMM (Unweighted)</td>
<td><a href="./tracks/FATHMM_U.bw">bigWig</a></td>
</tr>
<tr>
<td>FATHMM_W</td>
<td>FATHMM (Weighted)</td>
<td><a href="./tracks/FATHMM_W.bw">bigWig</a></td>
</tr>
<tr>
<td>MA</td>
<td>Mutation Assessor</td>
<td><a href="./tracks/MA.bw">bigWig</a></td>
</tr>
<tr>
<td>MT</td>
<td>MutationTaster</td>
<td><a href="./tracks/MT.bw">bigWig</a></td>
</tr>
<tr>
<td>VEST</td>
<td>VEST</td>
<td><a href="./tracks/VEST.bw">bigWig</a></td>
</tr>
<tr>
<td>PROVEAN</td>
<td>PROVEAN</td>
<td><a href="./tracks/PROVEAN.bw">bigWig</a></td>
</tr>
<tr>
<td>LRT</td>
<td>LRT</td>
<td><a href="./tracks/LRT.bw">bigWig</a></td>
</tr>
<tr>
<td>MetaLR</td>
<td>MetaLR</td>
<td><a href="./tracks/MetaLR.bw">bigWig</a></td>
</tr>
<tr>
<td>MetaSVM</td>
<td>MetaSVM</td>
<td><a href="./tracks/MetaSVM.bw">bigWig</a></td>
</tr>
<tr>
<td colspan=3>
<h3>Genome-Wide Prediction Algorithms</h3>
</td>
</tr>
<tr>
<td>FATHMM_MKLNC</td>
<td>FATHMM-MKL (Non-Coding)</td>
<td><a href="./tracks/FATHMM_MKLNC.bw">bigWig</a></td>
</tr>
<tr>
<td>CADD</td>
<td>CADD</td>
<td><a href="./tracks/CADD.bw">bigWig</a></td>
</tr>
<tr>
<td>DANN</td>
<td>DANN</td>
<td><a href="./tracks/DANN.bw">bigWig</a></td>
</tr>
<tr>
<td>PP46</td>
<td>PhyloP: based on the MSA of 45 vertebrate genomes to the human genome</td>
<td><a href="./tracks/PP46.bw">bigWig</a></td>
</tr>
<tr>
<td>PP100</td>
<td>PhyloP: based on the MSA of 99 vertebrate genomes to the human genome</td>
<td><a href="./tracks/PP100.bw">bigWig</a></td>
</tr>
<tr>
<td>PC46</td>
<td>PhastCons: based on the MSA of 45 vertebrate genomes to the human genome</td>
<td><a href="./tracks/PC46.bw">bigWig</a></td>
</tr>
<tr>
<td>PC100</td>
<td>PhastCons: based on the MSA of 99 vertebrate genomes to the human genome</td>
<td><a href="./tracks/PC100.bw">bigWig</a></td>
</tr>
<tr>
<td>GERP_RS</td>
<td>GERP++ Rejected Substitutions (RS Scores)</td>
<td><a href="./tracks/GERP_RS.bw">bigWig</a></td>
</tr>
<tr>
<td>GERP_CE</td>
<td>GERP++ Constrained Elements</td>
<td><a href="./tracks/GERP_CE.bw">bigWig</a></td>
</tr>
<tr>
<td colspan=3>
<h3>Cancer-Specific Prediction Algorithms</h3>
</td>
</tr>
<tr>
<td>FATHMM_C</td>
<td>FATHMM-Cancer</td>
<td><a href="./tracks/FATHMM_C.bw">bigWig</a></td>
</tr>
<tr>
<td>TFIC_SIFT</td>
<td>TransFIC (SIFT)</td>
<td><a href="./tracks/TFIC_SIFT.bw">bigWig</a></td>
</tr>
<tr>
<td>TFIC_PPH2</td>
<td>TransFIC (PolyPhen-2)</td>
<td><a href="./tracks/TFIC_PPH2.bw">bigWig</a></td>
</tr>
<tr>
<td>TFIC_MA</td>
<td>TransFIC (MutationAssessor)</td>
<td><a href="./tracks/TFIC_MA.bw">bigWig</a></td>
</tr>
</tbody>
</table>
<h2 id="tracks">Adding & Amending Tracks</h2>
<hr>
<p>
You can add additional tracks representing a range of computational prediction algorithms (please see the above list) using the <i class="fa fa-plus fa-border"></i> icon.
You can also add custom tracks, representing your own annotation data in bigWig and bigBed format, through the same option.
Once added to the browser, the appearance of tracks (e.g. color, height etc.) can be amended using the <i class="fa fa-road fa-border"></i> icon.
</p>
<h2 id="export">Exporting Images</h2>
<hr>
<p>
Once you are happy with the tracks displayed in the browser, publication quality images in SVG or PNG format can be generated using the <i class="fa fa-print fa-border"></i> icon.
</p>
<h2 id="response">Unresponsive Browser</h2>
<hr>
<p>
The Genome Tolerance Browser is a client-side JavaScript application. This means that all rendering is performed on your
web browser and not on our server. As a result, your browser may become slow or unresponsive when viewing large amounts of data.
Therefore, <b>we recommend that users remove all genome-wide prediction algorithms before zooming out too far or when searching for large genes.</b>
</p>
<h2 id="contact">Contact Us</h2>
<hr>
<p>
We welcome any comments or suggestions that you may have regarding our browser - please send an email directly to:
<script>
document.write('H.Shihab')
document.write('@bristol.ac.uk')
</script>
<br />
<br />
We also encourage developers of functional prediction algorithms wishing to include their algorithm in our browser to contact us.
</p>
<!-- add new content when required -->
<br />
<br />
</div>
</div>
</div>
</div>
<script src="./js/jquery.min.js"></script>
<script src="./js/bootstrap.min.js"></script>
<script>
$('#sidebar').affix({
offset: {
top: 235
}
});
var $body = $(document.body);
var navHeight = $('.navbar').outerHeight(true) + 10;
$body.scrollspy({
target: '#leftCol',
offset: navHeight
});
$('a[href*=#]:not([href=#])').click(function() {
if (location.pathname.replace(/^\//, '') == this.pathname.replace(/^\//, '') && location.hostname == this.hostname) {
var target = $(this.hash);
target = target.length ? target : $('[name=' + this.hash.slice(1) + ']');
if (target.length) {
$('html,body').animate({
scrollTop: target.offset().top - 50
}, 1000);
return false;
}
}
});
</script>
</body>
</html>