SwissOrthology

<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <title>SwissOrthology</title> <meta name="description" content="Compare hierarchical orthologous groups (HOGs) across the SIB orthology resources OMA and OrthoDB"> <meta name="viewport" content="width=device-width, initial-scale=1"> <link rel='icon' href="/static/favicon.ico" type='image/x-icon'/> <link rel="stylesheet" href="//stackpath.bootstrapcdn.com/bootstrap/4.3.1/css/bootstrap.min.css" integrity="sha384-ggOyR0iXCbMQv3Xipma34MD+dH/1fQ784/j6cY/iJTQUOhcWr7x9JvoRxT2MZw1T" crossorigin="anonymous"> <link href="//fonts.googleapis.com/icon?family=Material+Icons|Material+Icons+Outlined|Signika:300,400,600,700|Open+Sans:300,400,500,700" rel="stylesheet"> <link rel="stylesheet" href="/static/css/style.css"/> <style> [v-cloak] {display: none} </style>  <script> var _paq = window._paq = window._paq || []; /* tracker methods like "setCustomDimension" should be called before "trackPageView" */ _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u="https://matomo.sib.swiss/"; _paq.push(['setTrackerUrl', u+'matomo.php']); _paq.push(['setSiteId', '53']); var d=document, g=d.createElement('script'), s=d.getElementsByTagName('script')[0]; g.async=true; g.src=u+'matomo.js'; s.parentNode.insertBefore(g,s); })(); </script>  </head> <body> <nav class="navbar navbar-expand-md navbar-light bg-light bg-lightest"> <div class="container"> <a class="sib-logo" href="https://www.sib.swiss" target="_blank"> <img src="/static/image/logo-sib.png" alt="Logo SIB" /> </a> <a class="navbar-brand" href="/service/search"> <img alt="SwissOrthology" src="/static/image/logo-swiss-orthology.svg"> </a>  <div id="navbarNav"> <ul class="navbar-nav ml-auto"> <li class="nav-item"> <a class="nav-link" href="/service/search"> <img src="/static/image/home.svg"> Home <span class="sr-only">(current)</span> </a> </li> <li class="nav-item"> <a class="nav-link" href="/service/about"> <img src="/static/image/info.svg"> About </a> </li> <li class="nav-item"> <a class="nav-link" href="/service/guide"> <img src="/static/image/book-open.svg"> Guide </a> </li> <li class="nav-item"> <a class="nav-link" href="/service/events"> <img src="/static/image/calendar.svg"> Events </a> </li> </ul> </div> </div> </nav> <div id="app" class="content-container" v-cloak>   <div id="search-container"> <div class="container"> <div id="search-so"> <div id="searchMe" class="input-group"> <input v-model="term" class="form-control" type="search" placeholder="Search with UniProt accession" aria-label="Search" @keyup.enter="search"> <button @click="search" class="btn btn-so-search" type="button"><i class="material-icons">search</i></button> <p v-if="!is_level_result_valid"> Search for a UniProtKB Accession (e.g. <span @click="fillExample('P12345')">P12345</span>) to identify which method provide HOGs at which taxonomic range, and then to compare their members. </p> </div> <div v-if="searching" id="search-status"> <svg xmlns="http://www.w3.org/2000/svg" viewBox="0 0 117.1 62.37"> <g id="Layer_2" data-name="Layer 2"> <g id="Layer_1-2" data-name="Layer 1"> <g id="_Group_" data-name=" Group "> <path class="cls-1" d="M117.1,54.38h0l-.12-.33L93.61,19.67,87.32,31.94,79.17,18.36,72.88,27,61.72,0,43,28.28l-6-8.06L0,59.76l24.63,2.6a1.94,1.94,0,0,0,2.09-1.44L37,22.16,49,46.33,61.72,1.15,75.58,39.39l3.68-19.6L92.82,47q.65-12.33,1.26-24.67L112.2,53.21Z"/> </g> </g> </g> </svg> </div> <div class="alert alert-info" v-if="noResultsFound">Your query returned no results.</div> </div> </div> </div> <div class="content-block"> <div v-if="is_level_result_valid" class="card" style="margin-top: 1rem;"> <div class="card-body"> <template v-if="uniprot_protein_info"> <h4 class="card-title">Taxonomic Levels of HOGs for <a v-if="uniprot_protein_info" v-bind:href="[[uniprot_protein_info.query_url]]">[[level_query_result.query_id]]</a>  <template v-if="[[uniprot_protein_info.swissprot_id]]">([[uniprot_protein_info.swissprot_id]]) </template> [<a v-bind:href="[[uniprot_protein_info.tax_url]]">[[uniprot_protein_info.sciname]]</a>]</h4> [[uniprot_protein_info.fullname]] </template> <template v-else> <h4 class="card-title">Taxonomic Levels of HOGs for [[level_query_result.query_id]]</h4> </template> </div> <div v-if="level_query_result.failing_for.length" class="alert alert-danger"> <p>Service currently not available for <b>[[service_error_message]]</b></p> </div> <table class="table table-hover "> <thead> <tr> <th>Taxonomic Level</th> <th><div><span>HOG in OMA</span></div></th> <th><div><span>HOG in OrthoDB</span></div></th> </tr> </thead> <tbody v-for="(data, lev) in level_query_result.levels" :key="lev" v-on:click="load_group_members(lev)"> <tr class="result" v-bind:class="{'selected-row': lev === selected_level}"> <td>[[lev]]</td> <td><i v-if="data.OMA" class="material-icons-outlined md-18">check_box</i></td> <td><i v-if="data.OrthoDB" class="material-icons-outlined md-18">check_box</i></td> </tr> </tbody> </table> </div> <div v-if="is_group_member_result_valid" class="card" id="hog_member_result" style="margin-top: 1rem;"> <div class="card-body"> <h4 class="card-title">Orthologs predicted by OMA and OrthoDB for [[term]] at taxonomic level "[[ selected_level ]]"</h4> <div class="dropdown align-right"> <button class="btn btn-secondary dropdown-toggle" type="button" id="downloadMenuButton" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false"> <i class="material-icons-outlined md-18">cloud_download</i> Download Sequences </button> <div class="dropdown-menu" aria-labelledby="downloadMenuButton"> <button v-if="showColumn('OMA')" type="button" class="dropdown-item" v-on:click="loadSequences(['OMA'],'union')">by OMA</button> <button v-if="showColumn('OrthoDB')" type="button" class="dropdown-item" v-on:click="loadSequences(['OrthoDB'],'union')">by OrthoDB</button> <button v-if="showIntersectOrUnion()" type="button" class="dropdown-item" v-on:click="loadSequences(['OMA','OrthoDB'],'intersect')">by OMA and OrthoDB (intersection)</button> <button v-if="showIntersectOrUnion()" type="button" class="dropdown-item" v-on:click="loadSequences(['OMA','OrthoDB'],'union')">by OMA or OrthoDB (union)</button> </div> </div> <table id="hog_member_table" class="table table-header-rotated table-hover"> <thead> <tr> <th>Protein</th> <th>Species</th> <th>Taxon ID</th> <th v-if="showColumn('OMA')" class="rotate-45"><div><span>Orthologs in OMA</span></div></th> <th v-if="showColumn('OrthoDB')" class="rotate-45"><div><span>Orthologs in OrthoDB</span></div></th> </tr> </thead> <tbody> <tr v-for="result in results.members" class="result"> <td><a v-bind:href="result.xref.uri">[[result.xref.id]]</a></td> <td>[[result.sciname]]</td> <td><a v-bind:href="result.taxon.uri">[[result.taxon.id]]</a></td> <td v-if="showColumn('OMA')"> <template v-if="!result.OMA"><i class="material-icons-outlined md-18">check_box_outline_blank</i></template> <template v-else-if="result.OMA.species_missing"></template> <template v-else><a v-bind:href="result.OMA.uri" target="_blank"><i class="material-icons-outlined md-18">check_box</i></a></template> </td> <td v-if="showColumn('OrthoDB')"> <template v-if="!result.OrthoDB"><i class="material-icons-outlined md-18">check_box_outline_blank</i></template> <template v-else-if="result.OrthoDB.species_missing"></template> <template v-else><a v-bind:href="result.OrthoDB.uri" target="_blank"><i class="material-icons-outlined md-18">check_box</i></a></template> </td> </tr> </tbody> </table> </div> </div> </div> <template v-if="!is_level_result_valid"> <div id="so-partners"> <div class="container"> <h4>Key resources</h4> <a href="https://omabrowser.org" target="_blank"><img src="/static/image/logo-oma.png" alt="OMA Browser" /></a> <a href="https://www.orthodb.org" target="_blank"><img src="/static/image/logo-orthodb.png" alt="OrthoDB" /></a> <a href="https://orthology.benchmarkservice.org" target="_blank"><img src="/static/image/logo-orthology-benchmark.png" alt="Orthology Benchmarking" /></a> <a href="https://busco.ezlab.org/" target="_blank"><img src="/static/image/logo-BUSCO.png" alt="BUSCO" /></a> <a href="https://omark.omabrowser.org" target="_blank"><img src="/static/image/logo-OMArk.png" alt="OMArk" /></a> </div> </div> <div class="container" id="home_info"> <div class="row"> <div class="col-md-6"> <div class="card"> <h1>What is <span class="red">Swiss</span>Orthology?</h1> <h4>SwissOrthology provides a unified entry point to orthology resources from <a href="https://sib.swiss">SIB</a>. </h4> <p>Under the SwissOrthology umbrella the SIB provides a variety of resources centered around orthology. Orthologs are genes that have started diverging through a speciation event. As they have been by definition the same gene until speciation, orthologs play an important role in many bioinformatics applications such as gene function prediction, species tree reconstruction or comparative analyses.</p> <p>SwissOrthology is a collaboration between the two research labs run by <a href="https://lab.dessimoz.org">Christophe Dessimoz at University Lausanne</a> and <a href="http://cegg.unige.ch/">Evgeny Zdobnov at University of Geneva</a>. The two labs develop and maintain two of the world leading resources for orthology: <a href="https://omabrowser.org"><strong>O</strong>rthologous <strong>MA</strong>trix</a> and <a href="https://www.orthodb.org/">OrthoDB</a>.</p> <p><a href="/service/about">Find out more</a> about the collaboration.</p> </div> </div> <div class="col-md-6"> <div class="card"> <h1>Interactive Guide</h1> <h4>Interactive Guide how to choose Orthology Resource</h4> <p>In the <a href="/service/guide">interactive guide</a> we try to help you to find the right orthology resource for your application.</p> </div> </div> </div> </div> </template> </div> <script src="https://cdn.jsdelivr.net/npm/vue@2"></script> <script src="/static/js/search.js"></script> <noscript> <img referrerpolicy="no-referrer-when-downgrade" src="https://matomo.sib.swiss/matomo.php?idsite=51&rec=1&action_name=non-js-access" style="border:0" alt="" /> </noscript>> <script src="//cdnjs.cloudflare.com/ajax/libs/jquery/3.3.1/jquery.min.js" integrity="sha256-FgpCb/KJQlLNfOu91ta32o/NMZxltwRo8QtmkMRdAu8=" crossorigin="anonymous"></script> <script src="//cdnjs.cloudflare.com/ajax/libs/popper.js/1.14.7/umd/popper.min.js" crossorigin="anonymous"></script> <script src="//stackpath.bootstrapcdn.com/bootstrap/4.3.1/js/bootstrap.min.js" integrity="sha384-JjSmVgyd0p3pXB1rRibZUAYoIIy6OrQ6VrjIEaFf/nJGzIxFDsf4x0xIM+B07jRM" crossorigin="anonymous"></script>  <script async src="https://www.googletagmanager.com/gtag/js?id=UA-136590259-1"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-136590259-1'); </script> </body> </html>

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SwissOrthology