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<!DOCTYPE html>
<html lang="en">
<head>
<!-- BootStrap template from http://themes.3rdwavemedia.com/demo/devaid/ -->
<title>Online Prediction of Human Whole Proteome Linkages</title>
<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="description" content="Online prediction of whole proteome linkages" />
<meta name="author" content="Yulong Niu" />
<meta name="keywords" content="whole genome,linkages,interactions,prediction" />
<link href='http://fonts.googleapis.com/css?family=Lato:300,400,300italic,400italic' rel='stylesheet' type='text/css'>
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<!-- ******HEADER****** -->
<header id="header" class="header">
<div class="container">
<h1 class="logo pull-left">
<a class="scrollto" href="#promo">
<span class="logo-title">PrePhyloPro</span>
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<li class="nav-item"><a class="scrollto" href="#about">About</a></li>
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<!-- ******PROMO****** -->
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<div class="container text-center">
<h2 class="title">Pre<span class="highlight">PhyloPro</span></h2>
<p class="intro">Online prediction of whole proteome linkages
based on phylogenetic profiles</p>
<div class="btns">
<a class="btn btn-cta-secondary" href="./ExampleData/ppp_hsafatpf1/index.html" target="_blank">Demo</a>
<a class="btn btn-cta-primary" href="#docs">Start Now!</a>
</div>
<div class="version">
<p>Current Version 1.0.1 (December 5, 2017)</p>
</div>
<ul class="meta list-inline">
<li><a href="https://github.com/YulongNiu/PhyloProfileWeb" target="_blank">View on GitHub</a></li>
<li><a href="https://github.com/YulongNiu/PhyloProfileWeb/blob/master/readme.md" target="_blank">Full Documentation</a></li>
<li>Created by: <a href="http://yulongniu.bionutshell.org/" target="_blank">Yulong Niu</a></li>
</ul><!--//meta-->
</div><!--//container-->
</section><!--//promo-->
<!-- ******ABOUT****** -->
<section id="about" class="about section">
<div class="container">
<h2 class="title text-center">What is PrePhyloPro?</h2>
<p class="intro text-center">PrePhyloPro is an online tool for whole proteome linkages prediction. The predicted linkages reveal the direct or indirect connections. It can be used to detect novel physical protein-protein interactions, new components of biological complexes, and potential linkages in signaling pathways or metabolic processes. The internal algorithm is based on phylogenetic profiles which show genes occurence (presence or absence) in different species.</p>
<div class="row">
<div class="item col-md-4 col-sm-6 col-xs-12">
<div class="icon-holder">
<i class="fa fa-crosshairs"></i>
</div>
<div class="content">
<h3 class="sub-title">High accuracy</h3>
<p>Higher accuracy compared with single co-occurrency (Jaccard similarity, Pearson correlation coefficient, and mutual information) and module-based methods.</p>
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<i class="fa fa-heart"></i>
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<h3 class="sub-title">Easy-to-use</h3>
<p>Only a data table in the <a href="./ExampleData/ppp_hsafatp1/atpSubOne.txt" target="_blank">txt</a> or <a href="./ExampleData/ppp_hsafatp1/atpSubOne.csv" target="_blank">csv</a> format is all you need to prepare. Additional webpage entering parameters are supported for advanced usage. </p>
</div><!--//content-->
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<div class="icon-holder">
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</div>
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<h3 class="sub-title">High quality figures</h3>
<p><a href="./ExampleData/ppp_hsafatp1/index.html" target="_blank">Outputs</a> are user-friendly visualized online and could be easily downloaded and restored on local computers. High quality figures and formatted tables are provided for academic publication.</p>
</div><!--//content-->
</div><!--//item-->
<div class="clearfix visible-md"></div>
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<div class="icon-holder">
<i class="fa fa-database"></i>
</div>
<div class="content">
<h3 class="sub-title">Extensive datasets</h3>
<p>Profiles were construced from 972 different species containing 276 eukaryotic, 614 bacterial, and 82 archaea species, and mitochondrial and chloroplast proteins were also included.</p>
</div><!--//content-->
</div><!--//item-->
<div class="item col-md-4 col-sm-6 col-xs-12">
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<i class="fa fa-code"></i>
</div>
<div class="content">
<h3 class="sub-title">open source</h3>
<p>Free and open source to all academic users. Internal data including phylogenetic profiles and gene annotation are downloadable. The prediction algorithm is open and hosted in <a href="https://github.com/YulongNiu/PhyloProfileWeb" target="_blank">GitHub</a>.</p>
</div><!--//content-->
</div><!--//item-->
<div class="item col-md-4 col-sm-6 col-xs-12">
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</div>
<div class="content">
<h3 class="sub-title">More...</h3>
<p><a href="http://d3js.org/" target="_blank">D3-based</a> interactive network visualization. Pathway analysis of predicted partners will be further supported. More organisms will be supported.</p>
</div><!--//content-->
</div><!--//item-->
</div><!--//row-->
</div><!--//container-->
</section><!--//about-->
<!-- ******FEATURES****** -->
<section id="features" class="features section">
<div class="container text-center">
<h2 class="title">New features</h2>
<ul class="feature-list list-unstyled">
<li><i class="fa fa-check"></i> Interactive circos plot;</li>
<li><i class="fa fa-check"></i> Arabidopsis thaliana (thale cress) is supported with an example;</li>
<li><i class="fa fa-check"></i> <a target="_blank" href="./ExampleData/ppp_hsafatp1/index.html">Pre-defined</a> annotation of input genes;</li>
<li><i class="fa fa-check"></i> Options of BLAST Evalue threshold;</li>
<li><i class="fa fa-check"></i> Interactive d3 network;</li>
</ul>
<ul class="release list-inline">
<li>
<a href="https://github.com/YulongNiu/PhyloProfileWeb/releases" target="_blank">Full Release History</a>
</li>
</ul>
</div><!--//container-->
</section><!--//features-->
<!-- ******Example****** -->
<section id="examples" class="examples section">
<div class="container">
<div class="examples-inner">
<h2 class="title text-center">Examples</h2>
<div class="info">
<ul class="nav nav-tabs nav-justified">
<li class="active"><a data-toggle="tab" href="#Example1">Example 1</a></li>
<li><a data-toggle="tab" href="#Example2">Example 2</a></li>
<li><a data-toggle="tab" href="#Example3">Example 3</a></li>
<li role="presentation" class="dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#" role="button" aria-haspopup="true" aria-expanded="false">Bad Examples<span class="caret"></span></a>
<ul class="dropdown-menu">
<li><a href="#badex1" data-toggle="tab">Only one input gene</a></li>
</ul>
</li>
</ul>
<div class="tab-content">
<div id="Example1" class="tab-pane fade in active">
<h4 class="example-title">Human F1Fo-ATP synthase predicted linkages, ATP5E Circos plot</h4>
<table>
<tr>
<td>Click to see the example:</td>
<td>
<a class="btn btn-success" href="./ExampleData/ppp_hsafatp1/index.html" target="_blank">Example</a>
</td>
</tr>
<tr>
<td>
<br />
<br />
</td>
</tr>
<tr>
<td>Click to download example input files: </td>
<td>
<div class="btn-group">
<button type="button" class="btn btn-primary">Files</button>
<button type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<span class="caret"></span>
<span class="sr-only">Toggle Dropdown</span>
</button>
<ul class="dropdown-menu">
<li><a target="_blank" href="./ExampleData/ppp_hsafatp1/atpSubOne.txt">txt format</a></li>
<li role="separator" class="divider"></li>
<li><a target="_blank" href="./ExampleData/ppp_hsafatp1/atpSubOne.csv">csv format</a></li>
</ul>
</div>
</td>
</tr>
</table>
<h4 class="example-title">Citation:</h4>
<p>
Niu Y, Moghimyfiroozabad S, Safaie S, Yang Y, Jonas EA, Alavian KN (2017) <b>Phylogenetic Profiling of Mitochondrial Proteins and Integration Analysis of Bacterial Transcription Units Suggest Evolution of F1Fo ATP Synthase from Multiple Modules.</b> <i>J Mol Evol</i> 85: 219 <a href="https://doi.org/10.1007/s00239-017-9819-3" target="_blank">https://doi.org/10.1007/s00239-017-9819-3</a>
</p>
</div>
<div id="Example2" class="tab-pane fade">
<h4 class="example-title">Human F1Fo-ATP synthase predicted linkages, F1 Circos plot</h4>
<table>
<tr>
<td>Click to see the example:</td>
<td>
<a class="btn btn-success" href="./ExampleData/ppp_hsafatpf1/index.html" target="_blank">Example</a>
</td>
</tr>
<tr>
<td>
<br />
<br />
</td>
</tr>
<tr>
<td>Click to download example input files: </td>
<td>
<div class="btn-group">
<button type="button" class="btn btn-primary">Files</button>
<button type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<span class="caret"></span>
<span class="sr-only">Toggle Dropdown</span>
</button>
<ul class="dropdown-menu">
<li><a target="_blank" href="./ExampleData/ppp_hsafatpf1/atpSub.txt">txt format</a></li>
<li role="separator" class="divider"></li>
<li><a target="_blank" href="./ExampleData/ppp_hsafatpf1/atpSub.csv">csv format</a></li>
</ul>
</div>
</td>
</tr>
</table>
<h4 class="example-title">Citation:</h4>
<p>
Niu Y, Moghimyfiroozabad S, Safaie S, Yang Y, Jonas EA, Alavian KN (2017) <b>Phylogenetic Profiling of Mitochondrial Proteins and Integration Analysis of Bacterial Transcription Units Suggest Evolution of F1Fo ATP Synthase from Multiple Modules.</b> <i>J Mol Evol</i> 85: 219 <a href="https://doi.org/10.1007/s00239-017-9819-3" target="_blank">https://doi.org/10.1007/s00239-017-9819-3</a>
</p>
</div>
<div id="Example3" class="tab-pane fade">
<h4 class="example-title"><i>Arabidopsis</i> F1Fo-ATP synthase predicted linkages, ATP5 Circos plot</h4>
<table>
<tr>
<td>Click to see the example:</td>
<td>
<a class="btn btn-success" href="./ExampleData/ppp_athfatp1/index.html" target="_blank">Example</a>
</td>
</tr>
<tr>
<td>
<br />
<br />
</td>
</tr>
<tr>
<td>Click to download example input files: </td>
<td>
<div class="btn-group">
<button type="button" class="btn btn-primary">Files</button>
<button type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<span class="caret"></span>
<span class="sr-only">Toggle Dropdown</span>
</button>
<ul class="dropdown-menu">
<li><a target="_blank" href="./ExampleData/ppp_athfatp1/atpSub.txt">txt format</a></li>
<li role="separator" class="divider"></li>
<li><a target="_blank" href="./ExampleData/ppp_athfatp1/atpSub.csv">csv format</a></li>
</ul>
</div>
</td>
</tr>
</table>
<h4 class="example-title">Citation:</h4>
<p>
Niu Y, Moghimyfiroozabad S, Safaie S, Yang Y, Jonas EA, Alavian KN (2017) <b>Phylogenetic Profiling of Mitochondrial Proteins and Integration Analysis of Bacterial Transcription Units Suggest Evolution of F1Fo ATP Synthase from Multiple Modules.</b> <i>J Mol Evol</i> 85: 219 <a href="https://doi.org/10.1007/s00239-017-9819-3" target="_blank">https://doi.org/10.1007/s00239-017-9819-3</a>
</p>
</div>
<div id="badex1" class="tab-pane fade">
<h4 class="example-title">Only one input candicate genes</h4>
<table>
<tr>
<td>Click to download example input files: </td>
<td>
<div class="btn-group">
<button type="button" class="btn btn-primary">Files</button>
<button type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">
<span class="caret"></span>
<span class="sr-only">Toggle Dropdown</span>
</button>
<ul class="dropdown-menu">
<li><a target="_blank" href="./ExampleData/badExample/oneInput.txt">txt format</a></li>
</ul>
</div>
</td>
</tr>
</table>
</div>
</div><!-- example-table -->
</div><!--//info-->
<div class="cta-container">
<div class="speech-bubble">
<p class="intro">You are encouraged to share your own examples, we will be very happy to show them on this site. If you are interested, please compress the result files along with the citation information (PubMed ID, article links, or any other messages), and emails us. Thanks!</p>
<div class="icon-holder text-center"><i class="fa fa-smile-o"></i></div>
</div><!--//speech-bubble-->
<div class="btn-container text-center">
<a href="mailto: yulong.niu@aol.com"><i class="fa fa-envelope fa-2x"></i></a>
</div><!--//btn-container-->
</div><!--//cta-container-->
</div><!--//license-inner-->
</div><!--//container-->
</section><!--//how-->
<!-- ******DOCS****** -->
<section id="docs" class="docs section">
<div class="container">
<div class="docs-inner">
<form target="_blank" method="post" action="/cgi-bin/phyloCGI/linkage_predict.py" enctype="multipart/form-data">
<h2 class="title text-center">Get Started</h2>
<div class="block">
<h3 class="sub-title text-center">Step 1</h3>
<div class="step-block">
<h4 class="step-title">Algorithm parameters</h4>
<ul class="nav nav-tabs nav-justified">
<li class="active"><a data-toggle="tab" href="#linkNum">Linkages number</a></li>
<li><a data-toggle="tab" href="#blastThres">BLAST Evalue</a></li>
<li><a data-toggle="tab" href="#organism">Organism</a></li>
</ul>
<div class="tab-content">
<div id="linkNum" class="tab-pane fade in active">
<div class="input-group">
<div class="input-group-addon">1 ≤</div>
<input class="form-control" type="text" name="topNum" value="20"/>
<div class="input-group-addon">≤ 500</div>
</div><!-- input-group -->
<div class="tip-info">
<div class="alert alert-warning" role="alert">The smaller value, the less predicted linkages.</div>
</div><!-- tip-infor -->
</div><!-- linkage number -->
<div id="blastThres" class="tab-pane fade">
<div class="input-group">
<span class="input-group-addon">
<input type="radio" name="evalue" value="1e-03" checked="checked"/>
</span>
<input type="text" class="form-control" value="0.001" readonly/>
</div><!-- threshold -->
<div class="input-group">
<span class="input-group-addon">
<input type="radio" name="evalue" value="5e-04"/>
</span>
<input type="text" class="form-control" value="0.0005" readonly/>
</div><!-- threshold -->
<div class="input-group">
<span class="input-group-addon">
<input type="radio" name="evalue" value="1e-04"/>
</span>
<input type="text" class="form-control" value="0.0001" readonly/>
</div><!-- threshold -->
<div class="tip-info">
<div class="alert alert-warning" role="alert">The smaller value, the less homologs in the profile.</div>
</div><!-- tip-infor -->
</div><!-- blast threshold -->
<div id="organism" class="tab-pane fade">
<div class="input-group">
<span class="input-group-addon">
<input type="radio" name="org" value="hsa" checked="checked"/>
</span>
<input type="text" class="form-control" value="Homo sapiens (human)" readonly/>
</div><!-- hsa -->
<div class="input-group">
<span class="input-group-addon">
<input type="radio" name="org" value="ath"/>
</span>
<input type="text" class="form-control" value="Arabidopsis thaliana (thale cress)" readonly/>
</div><!-- ath -->
</div><!-- organism -->
</div>
</div><!-- step1-block-excute -->
</div><!--//step1-block-->
<div class="block">
<h3 class="sub-title text-center">Step 2</h3>
<div class="step-block">
<h4 class="step-title">Plot parameters</h4>
<ul class="nav nav-tabs nav-justified">
<li role="presentation" class="dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#" role="button" aria-haspopup="true" aria-expanded="false">Phylogenic plot<span class="caret"></span></a>
<ul class="dropdown-menu">
<li><a href="#profilefig" data-toggle="tab">Size of gene names</a></li>
</ul>
</li>
<li role="presentation" class="dropdown">
<a class="dropdown-toggle" data-toggle="dropdown" href="#" role="button" aria-haspopup="true" aria-expanded="false">Correlation plot<span class="caret"></span></a>
<ul class="dropdown-menu">
<li><a href="#corfig" data-toggle="tab">Size of gene names</a></li>
</ul>
</li>
</ul>
<div class="tab-content">
<div id="profilefig" class="tab-pane fade">
<div class="input-group">
<div class="input-group-addon">0 <</div>
<input class="form-control" type="text" name="phyloGeneNameSize" value='3.1'/>
</div> <!-- input-group -->
<div class="tip-info">
<div class="alert alert-warning" role="alert">The smaller value, the samller text size. <b>Tip: try the default value at first.</b></div>
</div> <!-- tip-infor -->
</div>
<div id="corfig" class="tab-pane fade">
<div class="input-group">
<div class="input-group-addon">0 <</div>
<input class="form-control" type="text" name="corGeneNameSize" value='3.1'/>
</div> <!-- input-group -->
<div class="tip-info">
<div class="alert alert-warning" role="alert">The smaller value, the samller text size. <b>Tip: try the default value at first.</b></div>
</div> <!-- tip-infor -->
</div>
</div>
</div><!-- step2-block-excute -->
</div><!--//step2-block-->
<div class="block">
<h3 class="sub-title text-center">Step 3</h3>
<div class="step-block">
<h4 class="step-title">Candidate gene list</h4>
<div class="input-group">
<input type="file" name="candidateList"/>
</div><!-- input-group -->
<div class="tip-info">
<div class="alert alert-warning" role="alert">The <a href="./ExampleData/ppp_hsafatp1/atpSubOne.txt" target="_blank">txt</a> or <a href="./ExampleData/ppp_hsafatp1/atpSubOne.csv" target="_blank">csv</a> format is supported.</div>
</div> <!-- tip-infor -->
</div><!-- step3-block-excute -->
</div><!--//step3-block-->
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<button type="submit" value="Submit" class="btn btn-success">Submit</button>
</div><!-- submit -->
</form><!-- form -->
<div class="block">
<h3 class="sub-title text-center">Full Documentation</h3>
<p>More details about setting paramters, file formats, and source codes are hosted on GitHub. </p>
<p class="text-center">
<a class="btn btn-cta-primary" href="https://github.com/YulongNiu/PhyloProfileWeb/blob/master/readme.md" target="_blank">More on GitHub</a>
</p>
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<h2 class="title text-center">Contact</h2>
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<p>I hope you find <b>PrePhyloPro</b> useful. Feel free to get in touch if you have any questions or suggestions. </p>
<p>If any unexpected results return (like an error webpage), please compress your input files and email us.</p>
<br/>
<p><strong>Citation:</strong></p>
<p>Niu Y, Liu C, Moghimyfiroozabad S, Yang Y, Alavian KN. (2017) <b>PrePhyloPro: phylogenetic profile-based prediction of whole proteome linkages</b>. <i>PeerJ</i> 5:e3712 <a href="https://doi.org/10.7717/peerj.3712" target="_blank">https://doi.org/10.7717/peerj.3712</a></p>
<div class="source">
<span class="name">Yulong Niu</span>
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<li><a href="http://alavianlab.org/" target="_blank"><i class="fa fa-flask"></i></a></li>
<li><a href="http://life.scu.edu.cn/webContent.asp?id=965&type=shiziduiwu" target="_blank"><i class="fa fa-university"></i></a></li>
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