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index.html
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<!DOCTYPE html>
<html lang='en'>
<head>
<meta charset='utf-8'>
<meta name='viewport' content='width=device-width, initial-scale=1'>
<link rel='stylesheet' href='https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css'>
<link rel='stylesheet' href='stylesheet/eorna.css'>
<link rel='icon' href='images/eorna-mini-logo.png'>
<title>EoRNA - Home</title>
<script src='https://ajax.googleapis.com/ajax/libs/jquery/3.5.1/jquery.min.js'></script>
<script src='https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js'></script>
<script src='https://cdn.plot.ly/plotly-latest.min.js'></script>
</head>
<body class='body-pos' data-spy='scroll' data-target='#list-data' data-offset='0' id='content'>
<div class="container-fluid">
<div class="row">
<nav class="col-md-2 d-none d-md-block sidebar grey">
<div class="sidebar-sticky">
<ul class="nav flex-column">
<li class="nav-item nav-link" id="nav-title"><img class="rounded mx-auto d-block" src='images/eorna-logo.png' width=150><span class='app-title'></li>
<li class="nav-item nav-link" id="nav-header"><b>Utilities Menu</b></li>
<div class="list-group">
<li class="nav-item"><a class="nav-link active" href="index.html">Home</a></li>
<li class="nav-item"><a class="nav-link" href="blast.html">Homology Search</a></li>
<li class="nav-item"><a class="nav-link" href="keyword.html">Annotation Search</a></li>
<li class="nav-item"><a class="nav-link" href="download.html">Bulk Data Download</a></li>
<li class="nav-item"><a class="nav-link" href="bart_lookup.html">Translate HORVU to BART IDs</a></li>
</div>
<li class="nav-item nav-link" id="nav-title"></li>
<li class="nav-item nav-link" id="nav-header"><b>Links</b></li>
<li class="nav-item nav-link" id="nav-title"></li>
<li class="nav-item"><a class="nav-link ext-links" href='contact.html'>Citation / About Authors</a></li>
<li class="nav-item"><a class="nav-link ext-links" href='http://ics.hutton.ac.uk/barleyrtd'>BarleyRTD Website</a></li>
<li class="nav-item"><a class="nav-link ext-links" href='http://ics.hutton.ac.uk'>Information and Computing Sciences @Hutton</a></li>
<li class="nav-item"><a class="nav-link ext-links" href='http://www.hutton.ac.uk'>The James Hutton Institute</a></li>
<li class="nav-item"><a class="nav-link ext-links" href='https://www.barleyhub.org/'>International Barley Hub</a></li>
<li class="nav-item nav-link" id="nav-title"></li>
<li class="nav-item nav-link" id="nav-header"><b>Funders</b></li>
<li class="nav-item nav-link" id="nav-title"></li>
<li class="nav-item nav-link" id="nav-title"><img class="rounded mx-auto d-block" src='images/nsf.png' width=150></li>
</ul>
</div>
</nav>
<main role="main" class="col-md-9 ml-sm-auto col-lg-10 pt-3 px-4">
<div class='data-body'>
<div class="card-deck mb-3">
<div class='card grey-card'>
<div class='card-header option-header'>Introduction</div>
<img src='images/mormyro_gymno.png' class="card-img-top">
<div class='card-body'>
<p><font color='#5c5f58'><b>EoRNA</b></font> is a Barley Expression Database that displays gene and transcript abundance data on demand as transcripts per million (TPM) across all samples and all the genes. </p>
<p><font color='#5c5f58'><b>EoRNA</b></font> provides access to the <a href='http://ics.hutton.ac.uk/barleyrtd'>Barley Reference Transcript Dataset</a> (BART), which consists of 177,240 unique barley expressed transcripts covering 60,444 genes. The transcripts are arranged as gene models and homology of the longest transcript to <i>Arabidopsis</i>, Rice and <i>Brachypodium</i> is given.</p>
<p>
You can access data directly by searching for a particular sequence ID or by <a href='blast.html'>BLASTing a sequence</a> against the genomic contigs or transcript sequences using the BLAST page.</p>
<p>A table directly comparing the BART gene annotations with the Barley Pseudomolecules Annotation (HORVU 2017) can be downloaded from <a href="downloads/Match-Overlap_All_BART_HORVU_wholeChrCoords.xlsx">here</a>.</p>
<p>
If you don't have a DNA or protein sequence, you can use the <a href='keyword.html'>Annotation Search</a> of the BLAST annotations of the genes, which are available for the <a href='http://rice.plantbiology.msu.edu/index.shtml'>Rice Pseudo-peptides v6</a>, the <a href='http://www.arabidopsis.org'>TAIR Arabidopsis thaliana Pseudo-peptides v10</a>, and the <a href='http://www.plantgdb.org/XGDB/phplib/download.php?GDB=Bd'>Brachypodium distachyon Pseudo-peptides</a>.</p>
<p>This research was supported and developed by Scottish Government Rural and Environment Science and Analytical Services division (RESAS) and funding from the Biotechnology and Biological Sciences Research Council and ERC project 669182 ‘SHUFFLE’.</p>
</div>
</div>
<div class="card grey-card">
<div class="card-header option-header">Search for a Sequence by ID</div>
<div class="card-body">
<p>Currently <font color='#5c5f58'><b>EoRNA</b></font> contains both the Barley RTD (BART) transcripts (<a href='https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-019-6243-7'>publication here</a>) and the predicted transcripts from the Barley Pseudomolecules (HORVU 2017) (<a href='https://www.nature.com/articles/nature22043'>publication here</a>).</p>
<p><b>Barley RTD</b> : The predicted genes have the nomenclature "BART1_0-u00001". Transcript models are named after the the gene loci like "BART1_0-u00001.001".
<p><b>HORVU 2017 Pseudomolecules Annotation</b> : The predicted genes have the nomenclature "HORVU1Hr1G000010". Transcript models are named after the gene loci like "HORVU1Hr1G000010.1".
<br><br>
<table class='table-bordered' width='100%'><theader><tr><th>Dataset</th><th>Gene IDs</th><th># Genes</th><th> # Transcripts</th></tr></theader>
<tbody>
<tr><td>Barley RTD</td><td>BART1_0-u00001</td><td>60,444</td><td>177,240</td></tr>
<tr><td>HORVU 2017</td><td>HORVU1Hr1G000010</td><td>81,683</td><td>334,126</td></tr>
</tbody>
</table>
<br><br>
<p>Searching for a gene ID will return all the transcript models from that gene region. You can go directly to a gene or transcript by using this search box:</p>
<form action='search_ids.cgi' method='get'>
<div class="input-group mb-3">
<div class="input-group-prepend">
<span class="input-group-text">Search for Sequence ID</span>
</div>
<input type="text" class="form-control" name='seq_name' value='BART1_0-u00001' onfocus="this.value=''">
<div class="input-group-append"><input class='btn btn-secondary red-btn' type='submit' value='Search'></div>
</div>
</form>
</div>
</div>
</div>
<div class="card-deck mb-3">
<div class="card red-card">
<div class="card-header option-header">BLAST Search</div>
<div class="card-body">
Use a nucleotide or protein sequence to find similar transcripts or genome sequence with the online BLAST search form.
</div>
<div class="card-footer red-footer"><a href="blast.html" class='btn btn-secondary red-btn'>Go</a></div>
</div>
<div class="card red-card">
<div class="card-header option-header">Annotation Search</div>
<div class="card-body">
Search the annotation of the transcripts using keywords. Transcripts are annotated with best BLAST hits to the predicted proteins from rice, <i>Brachypodium</i> and <i>Arabidopsis</i>.
</div>
<div class="card-footer red-footer"><a href="keyword.html" class='btn btn-secondary red-btn'>Go</a></div>
</div>
<div class="card red-card">
<div class="card-header option-header">Bulk Download</div>
<div class="card-body">
Download datasets, including transcript sequences, GFF files, and GO annotation.
</div>
<div class="card-footer red-footer"><a href="download.html" class='btn btn-secondary red-btn'>Go</a></div>
</div>
<div class="card red-card">
<div class="card-header option-header">Translate a List</div>
<div class="card-body">
Translate a list of HORVU Genes to BART Genes based on their overlap on the reference genome. The whole comparison can be found <a href="downloads/Match-Overlap_All_BART_HORVU_wholeChrCoords.xlsx">here</a>.
</div>
<div class="card-footer red-footer"><a href="bart_lookup.html" class='btn btn-secondary red-btn'>Go</a></div>
</div>
<div class="card red-card">
<div class="card-header option-header">GO Enrichment</div>
<div class="card-body">
Details of how to do GO enrichment analysis with the BART dataset.
</div>
<div class="card-footer red-footer"><a href="go.html" class='btn btn-secondary red-btn'>Go</a></div>
</div>
</div>
</div>
</main>
</div>
</div>
</body>
</html>