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<!doctype html>
<html class="h-100">
<head>
<!-- Bootstrap core CSS -->
<link rel="stylesheet" href="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous">
<meta name="description" content="Search thousands of betacoronavirus sequences and explore results by virus, host, country, and more">
<meta name="keywords" content="SARS-CoV-2, COVID-19, betacoronavirus, nhmmer, Rfam, blast">
<meta name="twitter:card" content="summary_large_image" />
<meta name="twitter:title" content="Betacoronavirus sequence similarity search" />
<meta name="twitter:description" content="Search thousands of betacoronavirus sequences and explore results by virus, host, country, and more" />
<meta name="twitter:image" content="https://covid19sequencesearch.github.io/src/images/interface-example.png" />
<title>Betacoronavirus sequence similarity search</title>
</head>
<body class="d-flex flex-column h-100">
<header>
<div class="navbar navbar-dark navbar-expand-lg bg-dark box-shadow">
<div class="container d-flex justify-content-between">
<a href="#" class="navbar-brand d-flex align-items-center">
<strong>Betacoronavirus sequence similarity search</strong>
</a>
<div class="collapse navbar-collapse" id="navbarNav">
<ul class="navbar-nav">
<li class="nav-item">
<a class="nav-link" href="https://github.com/covid19sequencesearch/covid19sequencesearch.github.io/issues" target="_blank">Feedback 💬</a>
</li>
</ul>
</div>
</div>
</div>
</header>
<main role="main">
<div class="row">
<section class="jumbotron text-center col" style="padding: 10px">
<div class="container small" style="text-align: left!important;">
<p class="lead">Search <span id="database-size"></span> betacoronavirus sequences and explore results by virus, host, country, and more</p>
<p>
Enter a sequence to find similar betacoronavirus sequences using <a href="https://www.ncbi.nlm.nih.gov/pubmed/23842809" target="_blank">nhmmer</a> and explore the results using facets.
<br>
This website is produced and maintained by the <a href="https://rnacentral.org" target="_blank">RNAcentral</a> team at <a href="https://www.ebi.ac.uk" target="_blank">EMBL-EBI</a>.
<a href="https://www.ebi.ac.uk/about/news/service-news/new-tool-sequence-similarity-searches-coronaviruses" target="_blank">Learn more →</a>
</p>
<strong>FAQ</strong>
<ul class="list-inline" style="display: inline; margin-left: 10px;">
<li class="list-inline-item">
<a href="#" data-toggle="modal" data-target="#howDoesItWorkModal">
How does the search work?
</a>
</li>
<li class="list-inline-item">
<a href="#" data-toggle="modal" data-target="#blastModal">
How does this search compare with BLAST?
</a>
</li>
<li class="list-inline-item">
<a href="#" data-toggle="modal" data-target="#sourceModal">
Where do the sequences come from?
</a>
</li>
</ul>
<p style="margin-top: 5px;">
<strong>Let us know</strong> if you find this tool useful or notice any problems by <a href="https://github.com/covid19sequencesearch/covid19sequencesearch.github.io/issues" target="_blank">raising an issue on GitHub →</a>
</p>
<p class="lead font-weight-bold">Get started by clicking examples below</p>
</div>
</section>
</div>
<div class="container">
<betacoronavirus-sequence-search
databases='["betacoronavirus"]'
examples='[
{"description": "5' UTR fragment", "urs": "", "sequence": "ATATTAGGTTTTTACCTACCCAGGAAAAGCCAACCAACCTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAAAATCTGTGTAGCTGTCGCTCGGCTGCATGCCTAGTGCACCTACGCAGTATAAACAATAATAAACTTTACTGTCGTTGACAAGAAACGAGTAACTCGTCCCTCTTCTGCAGACTGCTTACGGTTTCGTCCGTGTTGCAGTCGATCATCAGCATACCTAGGTTTCGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTTCTTGGAATCAACGAGAAAACA"},
{"description": "3' UTR fragment", "urs": "", "sequence": "CCACACAAGGCAGAUGGGCUAUAUAAACGUUUUCGCUUUUCCGUUUACGAUAUAUAGUCUACUCUUGUGCAGAAUGAAUUCUCGUAACUACAUAGCACAAGUAGAUGUAGUUAACUUUAAUCUCACAUAGCAAUCUUUAAUCAGUGUGUAACAUUAGGGAGGACUUGAAAGAGCCACCACAUUUUCACCGAGGCCACGCGGAGUAUACAGUGAACAAUGCUAGGGAGAGCUGCCUAUAUGGAAGAGCCCUAAUGUGUAAAAUUAAUUUUAGUAGUGCUAUCCCCAUGUGAUUUUAAUAGCUUCUUAGGAGAAUGAC"},
{"description": "2019-nCoV_N1-F primer", "urs": "", "sequence": "GACCCCAAAATCAGCGAAAT"},
{"description": "2019-nCoV_N1-R primer", "urs": "", "sequence": "TCTGGTTACTGCCAGTTGAATCTG"}
]'
rfam="true"
customStyle='{
"hideUploadButton": "true"
}'
/>
</div>
<div class="container">
<div class="row">
<div class="col-md-12">
<!-- Modals -->
<div class="modal fade" id="blastModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5>Comparison with BLAST</h5>
</div>
<div class="modal-body">
<p>
This search uses the same sequences as <a href="https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&DATABASE=genomic/Viruses/Betacoronavirus" target="_blank">NCBI BLAST</a>, with the following differences:
<ul>
<li>Support for facets and keyword searches for exploring results</li>
<li>Use <em>nhmmer</em> as the search engine</li>
<li>Explore up to 1,000 top hits (compared to 100 in BLAST)</li>
<li>Integration with <a href="https://rfam.org/covid-19" target="_blank">Rfam</a> to annotate structured RNA elements</li>
</ul>
</p>
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<div class="modal fade" id="sourceModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5>Where do the sequences come from?</h5>
</div>
<div class="modal-body">
The sequences are regularly extracted from the <a href="https://ftp.ncbi.nlm.nih.gov/blast/db/Betacoronavirus.tar.gz" target="_blank">NCBI BLAST database</a> and the metadata is retrieved from the associated INSDC entries.
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
<div class="modal fade" id="howDoesItWorkModal" tabindex="-1" role="dialog" aria-labelledby="exampleModalLabel" aria-hidden="true">
<div class="modal-dialog">
<div class="modal-content">
<div class="modal-header">
<h5>How does the search work?</h5>
</div>
<div class="modal-body">
To support the research into SARS-CoV-2 and other betacoronaviruses, we adapted the infrastructure from the RNAcentral <a href="https://rnacentral.org/sequence-search" target="_blank">sequence similarity search</a> to query a set of betacoronavirus sequences using <a href="https://www.ncbi.nlm.nih.gov/pubmed/23842809" target="_blank">nhmmer</a> and explore the results using facets from <a href="https://www.ebi.ac.uk/ebisearch" target="_blank">EBI Search</a>.
</div>
<div class="modal-footer">
<button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</main>
<footer class="footer mt-auto py-3">
<div class="container">
<hr>
<a href="https://www.ebi.ac.uk">
<img src="https://ebi.emblstatic.net/web_guidelines/EBI-Framework/v1.3/images/logos/EMBL-EBI/EMBL_EBI_Logo_black.svg" style="width: 120px;">
</a>
<a href="https://www.covid19dataportal.org/">
<img src="https://www.covid19dataportal.org/assets/img/CV19DP_logo_oneliner2.svg" style="width: 200px; margin-left: 20px;">
</a>
<a href="https://rnacentral.org/">
<img src="https://rnacentral.org/static/img/logo/rnacentral_logo_dark_grey.png" style="width: 140px; margin-left: 10px;">
</a>
<a href="https://rfam.org/covid-19">
<img src="https://docs.rfam.org/en/latest/_static/rfam.png" style="width: 100px; margin-left: 10px;">
</a>
<a href="https://github.com/covid19sequencesearch/covid19sequencesearch.github.io" class="float-right">
<img src="https://github.githubassets.com/images/modules/logos_page/GitHub-Mark.png" style="width: 40px;">
</a>
</div>
</footer>
<!-- Sequence search JS -->
<script type="text/javascript" src="/covid19sequencesearch.github.io/dist/covid19-sequence-search.js"></script>
<script src="https://code.jquery.com/jquery-3.3.1.slim.min.js" integrity="sha384-q8i/X+965DzO0rT7abK41JStQIAqVgRVzpbzo5smXKp4YfRvH+8abtTE1Pi6jizo" crossorigin="anonymous"></script>
<script src="https://stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM" crossorigin="anonymous"></script>
<script>
var getJSON = function(url, callback) {
var xhr = new XMLHttpRequest();
xhr.open('GET', url, true);
xhr.responseType = 'json';
xhr.onload = function() {
var status = xhr.status;
if (status === 200) {
callback(null, xhr.response);
} else {
callback(status, xhr.response);
}
};
xhr.send();
};
(function() {
getJSON('https://wwwdev.ebi.ac.uk/ebisearch/ws/rest/rnacentral-covid?format=json',
function(err, data) {
if (err !== null) {
console.log('Failed to retrieve sequence count: ' + err);
} else {
document.getElementById('database-size').innerHTML = data.domains[0].indexInfos[0].value;
}
});
})();
</script>
<script type="text/javascript" src="/covid19sequencesearch.github.io/dist/covid19-sequence-search.js"></script></body>
</html>