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triticumHPI.php
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triticumHPI.php
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<!DOCTYPE html>
<html>
<head>
<meta charset="utf-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<meta name="description" content="Interolog-based protein-protein interactions between wheat and Puccinia species.">
<meta name="author" content="Raghav Kataria">
<!-- App Favicon -->
<link rel="shortcut icon" href="assets/images/gallery/favicon.ico">
<!-- App title -->
<title>Triticum-Puccinia interactions : TRustDB</title>
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window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-DCNJT2KP9D');
</script>
</head>
<body>
<!-- Navigation Bar-->
<nav class="navbar navbar-expand-lg navbar-light bg-light">
<div class="container-fluid pl-5">
<div class="row w-100 pl-4">
<div class="col">
<a class="" href="https://bioinfo.usu.edu">
<img src='assets/images/kaabil_logo.png' height="70" alt="">
</a>
</div>
<div class="col-5">
</div>
<div class="col-auto">
<!-- <a href="index.html"><img src='assets/images/gallery/wheat_fav.png' height="40px"></a> -->
<!-- <a href="index.html"><img src='assets/images/gallery/triticum_logo.png' height="75px"></a> -->
<a href="https://www.usu.edu/"><img src='assets/images/gallery/usu-logo1.png' height="70px"></a>
</div>
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<nav class="container-fluid usu-bg pl-5">
<div class="row py-3 pl-5">
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<div class="dropdown-menu" aria-labelledby="dropdownMenuButton">
<a class="dropdown-item" href="interolog-wheat.html">Interactomics</a>
<a class="dropdown-item" href="searchTrustDB.html">Advanced search module</a>
<a class="dropdown-item" href="blast-submittion.html">BLAST search</a>
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<i class="zmdi zmdi-format-list-bulleted"></i> Features
</div>
<div class="dropdown-menu" aria-labelledby="dropdownMenuButton">
<a class="dropdown-item" href="triticumHPI.php">Host-pathogen interactions</a>
<div class="dropdown-divider"></div>
<h6 class="ml-3" style="color:black"><b>Host</b></h6>
<a class="dropdown-item" href="transcriptionFactors.php">Transcription Factors</a>
<a class="dropdown-item" href="localizationHost.php">Subcellular Localization Annotations</a>
<a class="dropdown-item" href="geneontologyHost.php">Gene Ontology (GO) Term Annotations</a>
<a class="dropdown-item" href="domainsHost.php">Functional Domain Mappings (InterPro)</a>
<hr>
<h6 class="ml-3" style="color:black"><b>Pathogen</b></h6>
<a class="dropdown-item" href="ortholog.php"><i>Puccinia</i> species Orthologs</a>
<a class="dropdown-item" href="localization.php">Subcellular Localization Annotations</a>
<a class="dropdown-item" href="geneontology.php">Gene Ontology (GO) Term Annotations</a>
<a class="dropdown-item" href="domains.php">Functional Domain Mappings (InterPro)</a>
<a class="dropdown-item" href="effector.php">Effector Proteins</a>
<a class="dropdown-item" href="secretory.php">Secretory Proteins</a>
<a class="dropdown-item" href="effectors.php">Effector and Secretory Proteins</a>
</div>
</div>
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<a href="help.html" class="rk-nav-item"><i class="ion-document-text"></i> User guide </a>
</div>
<div class="col-auto ml-auto">
<form role="search" class="form-inline text-right">
<select class="form-control select2 mr-2" id="searchSelect">
<optgroup label="Puccinia species [Infecting Triticum]">
<option value="pug99">Puccinia graminis Ug99</option>
<option value="pgt21">Puccinia graminis 21-0</option>
</optgroup>
</select>
<input id="proteinTOsearch" placeholder="Search e.g: 'GMQ_00017T0'" class="form-control mr-2" type="text">
<a id="proteinSender" href=""><i class="fa fa-search" style="color:rgb(38, 92, 194)"></i></a>
</form>
</div>
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</nav>
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<h5 class="modal-title" id="exampleModalLabel">How this data was obtained?</h5>
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</button>
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<div class="modal-body">
<p>
The pre-calculated interactions were obtained by performing Interolog-based computational approach on <i>Triticum aestivum</i> and <i>Puccinia</i> proteomes.
</p>
<p>
<b>Step 1:</b> The whole proteomes of <i>T. aestivum</i> and <i>Puccinia</i> species were BLAST searched against the known (standard) protein-protein interaction databases (DIP, BioGRID, HPIDB, IntAct, MINT, PHI-base, and STRING).
</p>
<p>
<b>Step 2:</b> 112 BLAST parameter combinations were randomly generated on the basis of <u>sequence identity</u> (30%, 40%, 50%, 60%), <u>evalue</u> (1e-10, 1e-50, 1e-05, 1e-04, 1e-20, 1e-30, 1e-25), and <u>sequence coverage</u> (40%, 50%, 60%, 80%).
</p>
<p>
<b>Step 3:</b> The combination with <b>identity >= 30%, evalue <= 1e-04, and coverage >= 40%</b> was considered as the best combination as the highest number of <i>Puccinia</i> effector proteins were identified in the interactions predicted using this combination.
</p>
<hr>
<p>
We have also provided the respective interaction databases, in reference to which these interactions have been predicted.
</p>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<!-- Page-Title -->
<div class="row">
<div class="col-xl-8">
<h4 class="page-title"><i>Triticum aestivum</i> - <i>Puccinia</i> interactions <i class="zmdi zmdi-info-outline" style="font-size: 25px" data-toggle="modal" data-target="#modal"></i></h4>
</div>
</div>
<!-- end row -->
<div class="col-12">
<div class="card-box">
<!-- <div class="row">
<div class="col-md-5" id="speciesSelect" >
<select class="form-control select2" id="pseudomonasI" style="font-style: italic;">
<optgroup label="Host species [Susceptible]" >
<option value="Medicago sativa">Alfalfa</option>
</optgroup>
</select>
</div>
<div class="col-md-5" id="buttonSearch" >
<button type="button" class="btn btn-twitter waves-effect waves-light">
<span class="btn-label"><i class="zmdi zmdi-search"></i></span>Search
</button>
</div>
<div class="col-md-2" id="downloadDiv" hidden="true">
<a id="downloadQueryBtn" href="" target="_blank" class="btn btn-purple waves-effect waves-light"download> Download Result <i class="fa fa-download" style="font-size: 20px"></i></a>
</div>
</div> -->
<br>
<table id="tableEffectors" class="table" cellspacing="0" width="100%" style="font-size: 14px">
<thead class='thead-dark'>
<tr role="row">
<th>Host protein</th>
<th>Pathogen protein</th>
<th>Host species</th>
<th>Pathogen strain</th>
<th style="width: 140px;">Interaction database</th>
</tr>
</thead>
<?php
// Start the session
ini_set('display_errors', 1);
error_reporting(1);
require("config.php");
$species= $_POST['species'];
$namer= $_POST['namer'];
$outfile = "tmp/".$namer."_OutputQuery.txt";
$link = mysqli_connect('localhost:3306', DB_USER, DB_PASSWORD) or die('Could not connect to mysql');
$link->set_charset("utf8");
mysqli_select_db($link,'trustdb') or die('Could not select database');
$query = 'SELECT * FROM HPIinterolog';
// WHERE hostSpecies="'.$species.'"';
// print_r($query);
$result = mysqli_query($link,$query) or die('Query failed: ' . mysqli_error($link));
// $tabularFile = fopen($outfile, "w") or die("Unable to open file!");
while ($lineQueryResult = mysqli_fetch_array($result, MYSQLI_ASSOC)){
$triticumProtein = $lineQueryResult['hostProtein'];
$pucciniaProtein = $lineQueryResult['pathogenProtein'];
$hostSpecies = $lineQueryResult['hostSpecies'];
$pathogenSpecies = $lineQueryResult['pathogenSpecies'];
$source = $lineQueryResult['source'];
//$line = $triticumProtein ."\t". $pucciniaProtein ."\t". $hostSpecies."\t". $pathogenSpecies."\t". $source;
echo '<tr >';
echo '<td><a href="https://plants.ensembl.org/Multi/Search/Results?species=all;idx=;q=' . $triticumProtein . '" target="_blank"> ' .$triticumProtein.' </a></td>';
echo '<td><a href="https://fungi.ensembl.org/Multi/Search/Results?species=all;idx=;q=' . $pucciniaProtein . '" target="_blank">' . $pucciniaProtein . '</a></td>';
//echo '<td ">' . $pucciniaProtein . '</td>';
echo '<td ">' . $hostSpecies . '</td>';
echo '<td ">' . $pathogenSpecies . '</td>';
echo '<td ">' . $source . '</td>';
echo '</tr >';
// print_r($line);
// print_r('\n');
//
//fwrite($tabularFile, $line);
//fwrite($tabularFile, PHP_EOL);
}
mysqli_free_result($result);
mysqli_close($link);
//fclose($tabularFile);
// print_r($namer);
?>
</table>
</div>
</div> <!-- end row -->
</div> <!-- container -->
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<footer class="footer">
© 2022  |  <a href="https://www.usu.edu" target="_blank">Utah State University</a>  |  <a href="https://bioinfo.usu.edu" target="_blank">Kaundal Artificial Intelligence & Advanced Bioinformatics Laboratory</a>  |  <a href="https://www.psc.usu.edu" target="_blank">Department of Plants, Soils, and Climate</a>  |  <a href="https://www.biosystems.usu.edu" target="_blank">Center for Integrated BioSystems </a>
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<script src="assets/plugins/datatables/buttons.print.min.js"></script>
<script type="text/javascript">
$(document).ready(function() {
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buttons: [
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]
} );
} );
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