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<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <title>About</title> <meta name="description" content="OMA is a method and database for the inference of orthologs among complete genomes. Since 2004 it has been continuesly maintained and improved. We provide browsable orthology predictions, APIs, flat file downloads and a standalone version of the inference algorithm."> <meta name="viewport" content="width=device-width, initial-scale=1.0"> <meta name="keywords" content="orthology,evolutionary gene relations,evolution,paralogy,inference"> <!-- Matomo --> <script> var _paq = window._paq = window._paq || []; /* tracker methods like "setCustomDimension" should be called before "trackPageView" */ _paq.push(["setCookieDomain", "*.omabrowser.org"]); _paq.push(['trackPageView']); _paq.push(['enableLinkTracking']); (function() { var u="https://matomo.sib.swiss/"; _paq.push(['setTrackerUrl', u+'matomo.php']); _paq.push(['setSiteId', '6']); 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> <noscript><p><img src="https://matomo.sib.swiss/matomo.php?idsite=6&rec=1" style="border:0;" alt="" /></p></noscript> <!-- End Matomo Code --> <link rel="shortcut icon" href="/static/image/favicon.ico" type="image/x-icon"> <!-- css includes --> <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/bootstrap@4.6.2/dist/css/bootstrap.min.css"> <link rel="stylesheet" href="https://fonts.googleapis.com/css?family=Dosis:400,800%7CNoto+Sans:400,700%7CRopa+Sans%7CMaterial+Icons"> <link rel="stylesheet" href="https://fonts.googleapis.com/css2?family=Material+Symbols+Outlined:opsz,wght,FILL,GRAD@48,400,0,0"> <link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/4.1.3/css/bootstrap.min.css" integrity="sha256-eSi1q2PG6J7g7ib17yAaWMcrr5GrtohYChqibrV7PBE=" crossorigin="anonymous"> <link rel="stylesheet" href="/static/css/oma_styles.css"> <!-- js includes --> <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/twitter-bootstrap/4.1.3/js/bootstrap.bundle.min.js" integrity="sha256-E/V4cWE4qvAeO5MOhjtGtqDzPndRO1LBk8lJ/PR7CA4=" crossorigin="anonymous"></script> <script>const static_root = "/static/";</script> <!-- AA: not sure which of those libs will still be needed. I suspect autocomplete.min.js for sure, rest probably not --> <link rel="stylesheet" href="https://use.fontawesome.com/releases/v5.11.2/css/all.css"> <script src="/static/js/jquery.autocomplete.min.js"></script> <script id="release_char-data" type="application/json">"E"</script> </head> <body class=""> <nav class="navbar fixed-top navbar-expand-xl bg-light navbar-light topnav"> <div class="logos-navbar mr-auto"> <a href="https://www.sib.swiss/"><img src="/static/image/logo-SIB.png" alt="Logo SIB"/></a> <a href="/oma/home/"><img src="/static/image/logo-oma-mobile.svg" alt="Logo OMA small"/></a> </div> <span class="oma-main-search-header"> <script src="/static/js/vue.js"></script> <style> .button_search { cursor:pointer; align-self: center; height: 100%; background-color: transparent; border: none; margin-right: 4px; margin-left: auto; order: 2; } .button_search:disabled { cursor:not-allowed; } .help_icon { align-self: center; font-size: 1.5em; margin: 4px; cursor: pointer; } .prefix-dropdown { border: none; background-color: transparent; } .vl { border-left: 2px solid grey; margin-left: 4px; margin-right: 4px; } #search_nav_input_part { display: flex; border: 1px solid #eee; font-size: 0.9em; box-sizing: border-box; padding: 0 0 0 4px; border-radius: 500px; } .ml-input{} .sl-input{height: 50px;} .token-input__tag { height: 30px; display: inline-block; margin-right: 10px; background-color: #eee; margin-top: 10px; line-height: 30px; padding: 0 5px; border-radius: 5px; } .token-input__tag > span { cursor: pointer; opacity: 0.75; } .token-input__text { border: none; outline: none; font-size: 0.9em; line-height: 50px; flex-grow: 1; background: transparent; } .token-delete { margin-left: 4px; color: red; } #token-container_search_nav{ overflow: scroll; display: inline; } .ml-token-con{margin-bottom: 8px;} .sl-token-con{white-space: nowrap;} </style> <script type="module"> const {createApp} = Vue window.search_token_vue_search_nav = createApp({ data() { return { tokens: [], //{query: 'HUMAN', single_term: true, prefix: "Species", type: "Taxon"} prefixes: { 'Protein': ['proteinid','xref','go','ec','description','domain','sequence'], 'Taxon': ['species','taxid', 'taxon'], 'HOG': ['hog','sequence'], 'OMA_Group': ['og', 'fingerprint','sequence'], }, default_prefix : 'description', show_error: false, error_message : " Error.", post_query_search_nav: '', multiline: false, wild_card: 'sequence', placeholder: ' "Blue-light photoreceptor" | proteinid:P53_RAT | species:"Drosophila melanogaster" ', //'P53_RAT | Insulin | species:HUMAN | "auxin response factor"', placeholder_default: 'proteinid:P53_RAT | "Blue-light photoreceptor" | species:"Drosophila melanogaster" ' //'P53_RAT | Insulin | species:HUMAN | "auxin response factor"', } }, compilerOptions: { delimiters: ["$[", "]$"] }, methods: { get_list_prefixes(lowercase=false){ let lp = [].concat(...Object.values(this.prefixes)); if (lowercase){ lp = lp.map(element => {return element.toLowerCase();}); } return lp }, get_prefix_used(){ return this.tokens.map(x => this.get_type_prefix(x.prefix)); }, get_type_prefix(prefix){ for (var key in this.prefixes) { if (this.prefixes.hasOwnProperty(key)) { if (this.prefixes[key].includes(prefix.toLowerCase())){ return key } } } return null }, addToken(event) { event.preventDefault() let val = event.target.value.trim(); if (val.length === 0 && this.tokens.length > 0){ this.collect_token() // wanted to auto search if press and empty + token but post request miss post_query data } else { var sinle_term = val[0] !== '"'; var multi_term_closed = (val.length > 1 && val[val.length - 1] === '"') var has_prefix = val.includes(':') var prefix_end = val[val.length - 1] === ':' var p = has_prefix ? val.split(':')[0].toLowerCase() : this.default_prefix; // If prefix but not valid if (has_prefix && !this.get_list_prefixes(true).includes(p.toLowerCase())) { this.show_error = true; this.error_message = "Error: Incorrect prefix." return; } else { this.show_error = false; } // If something typed if (val.length > 0) { // Multiple word query if (!sinle_term) { // STOP if multiple not closed if (!multi_term_closed) { if (event.code === "Space") { event.target.value = val + ' ' } return } } // STOP if the prefix is fine and we are at : if (prefix_end) { return } // has a prefix if (has_prefix) { var tmp = val.split(':')[1].trim() sinle_term = tmp[0] !== '"'; multi_term_closed = (val.length > 1 && tmp[tmp.length - 1] === '"') // multiple term if (!sinle_term) { // STOP if not closed if (!multi_term_closed) { if (event.code === "Space") { event.target.value = val + ' ' } return } } val = tmp } if (this.validate_token(val.replaceAll('"', ''), sinle_term, p)) { val = val.replaceAll('"', '') this.tokens.push({ query: val, single_term: sinle_term, prefix: p, type: this.get_type_prefix(p) }); event.target.value = ''; } } } document.getElementById("token-container_search_nav").scrollLeft += 200000; }, addToken_and_search(event){ this.addToken(event); if (this.tokens.length > 0){ this.collect_token() this.$refs.submit_button.click(); } }, removeToken(index) { this.tokens.splice(index, 1) }, removeLastToken(event) { if (event.target.value.length === 0) { this.removeToken(this.tokens.length - 1) } }, enter_from_input(event) { if (event.target.value.trim().length > 0) {this.addToken(event)} else{ event.target.nextElementSibling.focus().click() } }, collect_token(){ this.post_query_search_nav = JSON.stringify(this.tokens) }, detokenize(index){ var token = this.tokens.splice(index, 1)[0]; var input_token_search = document.getElementById('input_token_search_search_nav'); var token_str = token.prefix + ': ' token_str += token.single_term ? '' : '"' token_str += token.query token_str += token.single_term ? '' : '"' input_token_search.value = token_str }, on_change_prefix(target, t){ var prefix = target.value if (this.validate_token(t.query, t.single_term,prefix, true)){ t.prefix = prefix.toLowerCase() } else { target.value = t.prefix; } }, validate_token(val, sinle_term, p , OnChange=false){ if (this.wild_card.includes(p)){ return true } // todo Validate type val is valid for p // validate prefix not in conflict with other prefix var pu = this.get_prefix_used(); var current_prefix_type = this.get_type_prefix(p) if (current_prefix_type !== 'Taxon'){ var no_taxon = pu.filter(x => x !== 'Taxon'); if (no_taxon.length == 0){return true} else if (OnChange && no_taxon.length == 1){return true} else if (no_taxon.length > 0 && no_taxon.includes(current_prefix_type) ){return true} else if (no_taxon.length > 0 && !no_taxon.includes(current_prefix_type)) { this.show_error = true; this.error_message = "Warning: You are searching for " + no_taxon[0] + "; you can't add a token for " + current_prefix_type return false } } return true }, preload_token(tokens){ this.tokens = [] for (var i in tokens) { var token = tokens[i] if (this.validate_token(token.query, token.sinle_term, token.prefix )){ this.tokens.push({query: token.query, single_term: token.sinle_term, prefix: token.prefix, type:token.type}); } } this.placeholder = ''; this.$refs.input_handle.focus(); }, is_empty(){return this.tokens.length === 0}, modal_clicked(){ $('#exampleModal_search_nav').modal('show') }, format_token_string(str){ if (str.length < 20){return str} return str.slice(0, 20) + '...' } }, }).mount('#search_nav') var autocomplete_opts = { paramName: 'search', serviceUrl: '/api/xref/', minChars: 3, triggerSelectOnValidInput: false, deferRequestBy: 200, transformResult: function (response) { var json = JSON.parse(response); var xref_source_order = ['UniProtKB/SwissProt', 'UniProtKB/TrEMBL', 'Ensembl Protein', 'Ensembl Gene', 'Ensembl Transcript', 'RefSeq', 'EntrezGene', 'FlyBase', 'WormBase', 'EnsemblGenomes', 'NCBI', 'EMBL', 'SourceID', 'SourceAC', 'HGNC', 'Gene Name', 'Synonym', 'Protein Name', 'ORF Name', 'Ordered Locus Name', 'PDB', 'Swiss Model', 'STRING', 'neXtProt', 'Bgee', 'EPD', 'ChEMBL', 'GlyConnect', 'SwissPalm', 'DisGeNET', 'WikiGene', 'IPI', 'GI', 'n/a']; json.sort(function (a, b){ const idx_a = xref_source_order.indexOf(a.source), idx_b = xref_source_order.indexOf(b.source); if (idx_a === idx_b){ return a.xref > b.xref ? 1 : -1; } return idx_a - idx_b; }); return { suggestions: $.map(json, function (dataItem) { return {value: dataItem.xref, data: dataItem}; }) }; }, groupBy: 'source', formatResult: function(suggestion, currentValue) { // Do not replace anything if there current value is empty if (!currentValue) { return suggestion.value; } // escape any special char var pattern = '(' + currentValue.replace(/[|\\{}()[\]^$+*?.]/g, "\\$&") + ')'; var highlight_and_escape = function(val){ return val.replace(new RegExp(pattern, 'gi'), '<strong>$1<\/strong>') .replace(/&/g, '&') .replace(/</g, '<') .replace(/>/g, '>') .replace(/"/g, '"') .replace(/<(\/?strong)>/g, '<$1>'); }; return '<span class="auto-xref">' + highlight_and_escape(suggestion.data.xref) + '</span> ' + '<span class="auto-omaid">' + suggestion.data.omaid + '</span>' + '<span class="auto-species">' + highlight_and_escape(suggestion.data.genome.species) + '</span>'; }, onSelect: function(item){ window.location.href = "/oma/vps/" + item.data.entry_nr; return false; }, response: function( event, ui ) {console.log('HOG')} }; $('#input_token_search_search_nav').autocomplete(autocomplete_opts); </script> <!-- Modal --> <div class="modal fade" data-backdrop="false" id="exampleModal_search_nav" tabindex="-1" aria-labelledby="exampleModalLabelsearch_nav" aria-hidden="true"> <div class="modal-dialog modal-lg modal-dialog-centered" > <div class="modal-content"> <div class="modal-header"> <h4 class="modal-title" id="exampleModalLabelsearch_nav">How to use the search in OMA Browser ?</h4> <button type="button" class="close" data-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="modal-body" style="text-align: justify"> <strong>How does the search work?</strong> <p>Input a query in the search field. Everytime you press Space or Enter after a word, a <b>token</b> will be created. The token is composed of a <b>prefix</b> describing how the query should be treated and the actual <b>query</b> itself.</p> <strong>What are the different types of tokens?</strong> <p>Each token represents either a Gene, HOG, OMA group, or Taxon. Prefixes are used to specify which category to associate with the query term. </p> <table class="table table-bordered"> <thead> <tr> <th scope="col">Category</th> <th scope="col">Prefixes</th> </tr> </thead> <tbody> <tr> <th scope="row">Genes</th> <td>id, go, ec, description, domain, sequence</td> </tr> <tr> <th scope="row">HOGs</th> <td>hog, sequence</td> </tr> <tr> <th scope="row">OMA Groups</th> <td>omagroup, fingerprint, sequence</td> </tr> <tr> <th scope="row">Taxon</th> <td>species, taxid, taxon</td> </tr> </tbody> </table> <small>For example, the token [go:4225] will search for genes in the OMA database annotated with the GO:0004225 gene ontology term. </small> <br> <strong>How to search for a multi-word query?</strong> <p>If your query term is composed of multiple words (e.g homo sapiens), use " " to encapsulate it. </p> <strong>How many tokens can I have?</strong> <p>There is no limit on the number of tokens. It is not possible to enter multiple tokens of different categories, except taxon, which can be combined with other categories. For example, you can search for 'hog:60627 species:HUMAN' to return human genes found in HOG:606207. </p> <strong>How to edit/delete a token?</strong> <p>To edit a query, click on it to modify the input field. To edit a prefix, click on the dropdown icon to select another one. To remove a token, click on the x to delete it.</p> <strong>Autosuggest</strong> <p>Typing a query without hitting enter or space will prompt an autosuggestion for the identifier after a few seconds.</p> </div> <div class="modal-footer"> <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button> </div> </div> </div> </div> <form method="POST" id='form_' action="/oma/search-token/" > <input type="hidden" name="csrfmiddlewaretoken" value="EhFCpgV8JtmHNFs03pq5TNgdV6CaZVj0CKcGIochuCI5xDpSdMdrCZASAoWBIraA"> <div id="search_nav"> <div id="search_nav_input_part" :class="multiline ? 'ml-input' : 'sl-input'"> <span class="material-symbols-outlined help_icon" @click="modal_clicked"> help </span> <div id="token-container_search_nav" :class="multiline ? 'ml-token-con' : 'sl-token-con'" > <span v-for="token, index in tokens" :key="token" class="token-input__tag"> <select class="prefix-dropdown" @change="on_change_prefix($event.target, token)"> <template v-for="(prefixes_list, prefix_type) in prefixes"> <optgroup :label="prefix_type" > <option v-for="prefix in prefixes_list" :key="prefix" :selected="prefix == token.prefix"> $[ prefix ]$ </option> </optgroup> </template> </select> <span class="vl"></span> <p style="display: inline" @click='detokenize(index)'> $[ format_token_string(token.query) ]$ </p> <span @click='removeToken(index)' class="token-delete">X</span> </select> </span> </div> <input type="hidden" name="hidden_query" :value="post_query_search_nav"> <input type='text' :placeholder='placeholder' ref="input_handle" class='token-input__text' id="input_token_search_search_nav" @keydown.enter='enter_from_input' @keydown.space='addToken' @keydown.delete='removeLastToken' /> <button class=" button_search float-right" id="button_submit" ref="submit_button" :disabled="is_empty()" @click='collect_token()' type="submit"> <img style='width: 24px;' src="/static/image/logo-oma-o.svg" alt="Logo OMA icon"/> </button> </div> <div style="display: flex" v-show="show_error"> <small style="color: red; margin-right: auto;" > $[this.error_message]$ </small> </div> </div> </form> </span> <button type="button" class="navbar-toggler ml-auto collapsed" data-toggle="collapse" data-target="#bs-example-navbar-collapse-1"> <span></span> <span></span> <span></span> </button> <div class="collapse navbar-collapse" id="bs-example-navbar-collapse-1"> <div class="navbar-nav ml-auto"> <div class="search"> <h3>Search</h3> <script src="/static/js/vue.js"></script> <style> .button_search { cursor:pointer; align-self: center; height: 100%; background-color: transparent; border: none; margin-right: 4px; margin-left: auto; order: 2; } .button_search:disabled { cursor:not-allowed; } .help_icon { align-self: center; font-size: 1.5em; margin: 4px; cursor: pointer; } .prefix-dropdown { border: none; background-color: transparent; } .vl { border-left: 2px solid grey; margin-left: 4px; margin-right: 4px; } #search_min_input_part { display: flex; border: 1px solid #eee; font-size: 0.9em; box-sizing: border-box; padding: 0 0 0 4px; border-radius: 500px; } .ml-input{} .sl-input{height: 50px;} .token-input__tag { height: 30px; display: inline-block; margin-right: 10px; background-color: #eee; margin-top: 10px; line-height: 30px; padding: 0 5px; border-radius: 5px; } .token-input__tag > span { cursor: pointer; opacity: 0.75; } .token-input__text { border: none; outline: none; font-size: 0.9em; line-height: 50px; flex-grow: 1; background: transparent; } .token-delete { margin-left: 4px; color: red; } #token-container_search_min{ overflow: scroll; display: inline; } .ml-token-con{margin-bottom: 8px;} .sl-token-con{white-space: nowrap;} </style> <script type="module"> const {createApp} = Vue window.search_token_vue_search_min = createApp({ data() { return { tokens: [], //{query: 'HUMAN', single_term: true, prefix: "Species", type: "Taxon"} prefixes: { 'Protein': ['proteinid','xref','go','ec','description','domain','sequence'], 'Taxon': ['species','taxid', 'taxon'], 'HOG': ['hog','sequence'], 'OMA_Group': ['og', 'fingerprint','sequence'], }, default_prefix : 'description', show_error: false, error_message : " Error.", post_query_search_min: '', multiline: false, wild_card: 'sequence', placeholder: ' "Blue-light photoreceptor" | proteinid:P53_RAT | species:"Drosophila melanogaster" ', //'P53_RAT | Insulin | species:HUMAN | "auxin response factor"', placeholder_default: 'proteinid:P53_RAT | "Blue-light photoreceptor" | species:"Drosophila melanogaster" ' //'P53_RAT | Insulin | species:HUMAN | "auxin response factor"', } }, compilerOptions: { delimiters: ["$[", "]$"] }, methods: { get_list_prefixes(lowercase=false){ let lp = [].concat(...Object.values(this.prefixes)); if (lowercase){ lp = lp.map(element => {return element.toLowerCase();}); } return lp }, get_prefix_used(){ return this.tokens.map(x => this.get_type_prefix(x.prefix)); }, get_type_prefix(prefix){ for (var key in this.prefixes) { if (this.prefixes.hasOwnProperty(key)) { if (this.prefixes[key].includes(prefix.toLowerCase())){ return key } } } return null }, addToken(event) { event.preventDefault() let val = event.target.value.trim(); if (val.length === 0 && this.tokens.length > 0){ this.collect_token() // wanted to auto search if press and empty + token but post request miss post_query data } else { var sinle_term = val[0] !== '"'; var multi_term_closed = (val.length > 1 && val[val.length - 1] === '"') var has_prefix = val.includes(':') var prefix_end = val[val.length - 1] === ':' var p = has_prefix ? val.split(':')[0].toLowerCase() : this.default_prefix; // If prefix but not valid if (has_prefix && !this.get_list_prefixes(true).includes(p.toLowerCase())) { this.show_error = true; this.error_message = "Error: Incorrect prefix." return; } else { this.show_error = false; } // If something typed if (val.length > 0) { // Multiple word query if (!sinle_term) { // STOP if multiple not closed if (!multi_term_closed) { if (event.code === "Space") { event.target.value = val + ' ' } return } } // STOP if the prefix is fine and we are at : if (prefix_end) { return } // has a prefix if (has_prefix) { var tmp = val.split(':')[1].trim() sinle_term = tmp[0] !== '"'; multi_term_closed = (val.length > 1 && tmp[tmp.length - 1] === '"') // multiple term if (!sinle_term) { // STOP if not closed if (!multi_term_closed) { if (event.code === "Space") { event.target.value = val + ' ' } return } } val = tmp } if (this.validate_token(val.replaceAll('"', ''), sinle_term, p)) { val = val.replaceAll('"', '') this.tokens.push({ query: val, single_term: sinle_term, prefix: p, type: this.get_type_prefix(p) }); event.target.value = ''; } } } document.getElementById("token-container_search_nav").scrollLeft += 200000; }, addToken_and_search(event){ this.addToken(event); if (this.tokens.length > 0){ this.collect_token() this.$refs.submit_button.click(); } }, removeToken(index) { this.tokens.splice(index, 1) }, removeLastToken(event) { if (event.target.value.length === 0) { this.removeToken(this.tokens.length - 1) } }, enter_from_input(event) { if (event.target.value.trim().length > 0) {this.addToken(event)} else{ event.target.nextElementSibling.focus().click() } }, collect_token(){ this.post_query_search_min = JSON.stringify(this.tokens) }, detokenize(index){ var token = this.tokens.splice(index, 1)[0]; var input_token_search = document.getElementById('input_token_search_search_min'); var token_str = token.prefix + ': ' token_str += token.single_term ? '' : '"' token_str += token.query token_str += token.single_term ? '' : '"' input_token_search.value = token_str }, on_change_prefix(target, t){ var prefix = target.value if (this.validate_token(t.query, t.single_term,prefix, true)){ t.prefix = prefix.toLowerCase() } else { target.value = t.prefix; } }, validate_token(val, sinle_term, p , OnChange=false){ if (this.wild_card.includes(p)){ return true } // todo Validate type val is valid for p // validate prefix not in conflict with other prefix var pu = this.get_prefix_used(); var current_prefix_type = this.get_type_prefix(p) if (current_prefix_type !== 'Taxon'){ var no_taxon = pu.filter(x => x !== 'Taxon'); if (no_taxon.length == 0){return true} else if (OnChange && no_taxon.length == 1){return true} else if (no_taxon.length > 0 && no_taxon.includes(current_prefix_type) ){return true} else if (no_taxon.length > 0 && !no_taxon.includes(current_prefix_type)) { this.show_error = true; this.error_message = "Warning: You are searching for " + no_taxon[0] + "; you can't add a token for " + current_prefix_type return false } } return true }, preload_token(tokens){ this.tokens = [] for (var i in tokens) { var token = tokens[i] if (this.validate_token(token.query, token.sinle_term, token.prefix )){ this.tokens.push({query: token.query, single_term: token.sinle_term, prefix: token.prefix, type:token.type}); } } this.placeholder = ''; this.$refs.input_handle.focus(); }, is_empty(){return this.tokens.length === 0}, modal_clicked(){ $('#exampleModal_search_min').modal('show') }, format_token_string(str){ if (str.length < 20){return str} return str.slice(0, 20) + '...' } }, }).mount('#search_min') var autocomplete_opts = { paramName: 'search', serviceUrl: '/api/xref/', minChars: 3, triggerSelectOnValidInput: false, deferRequestBy: 200, transformResult: function (response) { var json = JSON.parse(response); var xref_source_order = ['UniProtKB/SwissProt', 'UniProtKB/TrEMBL', 'Ensembl Protein', 'Ensembl Gene', 'Ensembl Transcript', 'RefSeq', 'EntrezGene', 'FlyBase', 'WormBase', 'EnsemblGenomes', 'NCBI', 'EMBL', 'SourceID', 'SourceAC', 'HGNC', 'Gene Name', 'Synonym', 'Protein Name', 'ORF Name', 'Ordered Locus Name', 'PDB', 'Swiss Model', 'STRING', 'neXtProt', 'Bgee', 'EPD', 'ChEMBL', 'GlyConnect', 'SwissPalm', 'DisGeNET', 'WikiGene', 'IPI', 'GI', 'n/a']; json.sort(function (a, b){ const idx_a = xref_source_order.indexOf(a.source), idx_b = xref_source_order.indexOf(b.source); if (idx_a === idx_b){ return a.xref > b.xref ? 1 : -1; } return idx_a - idx_b; }); return { suggestions: $.map(json, function (dataItem) { return {value: dataItem.xref, data: dataItem}; }) }; }, groupBy: 'source', formatResult: function(suggestion, currentValue) { // Do not replace anything if there current value is empty if (!currentValue) { return suggestion.value; } // escape any special char var pattern = '(' + currentValue.replace(/[|\\{}()[\]^$+*?.]/g, "\\$&") + ')'; var highlight_and_escape = function(val){ return val.replace(new RegExp(pattern, 'gi'), '<strong>$1<\/strong>') .replace(/&/g, '&') .replace(/</g, '<') .replace(/>/g, '>') .replace(/"/g, '"') .replace(/<(\/?strong)>/g, '<$1>'); }; return '<span class="auto-xref">' + highlight_and_escape(suggestion.data.xref) + '</span> ' + '<span class="auto-omaid">' + suggestion.data.omaid + '</span>' + '<span class="auto-species">' + highlight_and_escape(suggestion.data.genome.species) + '</span>'; }, onSelect: function(item){ window.location.href = "/oma/vps/" + item.data.entry_nr; return false; }, response: function( event, ui ) {console.log('HOG')} }; $('#input_token_search_search_min').autocomplete(autocomplete_opts); </script> <!-- Modal --> <div class="modal fade" data-backdrop="false" id="exampleModal_search_min" tabindex="-1" aria-labelledby="exampleModalLabelsearch_min" aria-hidden="true"> <div class="modal-dialog modal-lg modal-dialog-centered" > <div class="modal-content"> <div class="modal-header"> <h4 class="modal-title" id="exampleModalLabelsearch_min">How to use the search in OMA Browser ?</h4> <button type="button" class="close" data-dismiss="modal" aria-label="Close"> <span aria-hidden="true">×</span> </button> </div> <div class="modal-body" style="text-align: justify"> <strong>How does the search work?</strong> <p>Input a query in the search field. Everytime you press Space or Enter after a word, a <b>token</b> will be created. The token is composed of a <b>prefix</b> describing how the query should be treated and the actual <b>query</b> itself.</p> <strong>What are the different types of tokens?</strong> <p>Each token represents either a Gene, HOG, OMA group, or Taxon. Prefixes are used to specify which category to associate with the query term. </p> <table class="table table-bordered"> <thead> <tr> <th scope="col">Category</th> <th scope="col">Prefixes</th> </tr> </thead> <tbody> <tr> <th scope="row">Genes</th> <td>id, go, ec, description, domain, sequence</td> </tr> <tr> <th scope="row">HOGs</th> <td>hog, sequence</td> </tr> <tr> <th scope="row">OMA Groups</th> <td>omagroup, fingerprint, sequence</td> </tr> <tr> <th scope="row">Taxon</th> <td>species, taxid, taxon</td> </tr> </tbody> </table> <small>For example, the token [go:4225] will search for genes in the OMA database annotated with the GO:0004225 gene ontology term. </small> <br> <strong>How to search for a multi-word query?</strong> <p>If your query term is composed of multiple words (e.g homo sapiens), use " " to encapsulate it. </p> <strong>How many tokens can I have?</strong> <p>There is no limit on the number of tokens. It is not possible to enter multiple tokens of different categories, except taxon, which can be combined with other categories. For example, you can search for 'hog:60627 species:HUMAN' to return human genes found in HOG:606207. </p> <strong>How to edit/delete a token?</strong> <p>To edit a query, click on it to modify the input field. To edit a prefix, click on the dropdown icon to select another one. To remove a token, click on the x to delete it.</p> <strong>Autosuggest</strong> <p>Typing a query without hitting enter or space will prompt an autosuggestion for the identifier after a few seconds.</p> </div> <div class="modal-footer"> <button type="button" class="btn btn-secondary" data-dismiss="modal">Close</button> </div> </div> </div> </div> <form method="POST" id='form_' action="/oma/search-token/" > <input type="hidden" name="csrfmiddlewaretoken" value="EhFCpgV8JtmHNFs03pq5TNgdV6CaZVj0CKcGIochuCI5xDpSdMdrCZASAoWBIraA"> <div id="search_min"> <div id="search_min_input_part" :class="multiline ? 'ml-input' : 'sl-input'"> <span class="material-symbols-outlined help_icon" @click="modal_clicked"> help </span> <div id="token-container_search_min" :class="multiline ? 'ml-token-con' : 'sl-token-con'" > <span v-for="token, index in tokens" :key="token" class="token-input__tag"> <select class="prefix-dropdown" @change="on_change_prefix($event.target, token)"> <template v-for="(prefixes_list, prefix_type) in prefixes"> <optgroup :label="prefix_type" > <option v-for="prefix in prefixes_list" :key="prefix" :selected="prefix == token.prefix"> $[ prefix ]$ </option> </optgroup> </template> </select> <span class="vl"></span> <p style="display: inline" @click='detokenize(index)'> $[ format_token_string(token.query) ]$ </p> <span @click='removeToken(index)' class="token-delete">X</span> </select> </span> </div> <input type="hidden" name="hidden_query" :value="post_query_search_min"> <input type='text' :placeholder='placeholder' ref="input_handle" class='token-input__text' id="input_token_search_search_min" @keydown.enter='enter_from_input' @keydown.space='addToken' @keydown.delete='removeLastToken' /> <button class=" button_search float-right" id="button_submit" ref="submit_button" :disabled="is_empty()" @click='collect_token()' type="submit"> <img style='width: 24px;' src="/static/image/logo-oma-o.svg" alt="Logo OMA icon"/> </button> </div> <div style="display: flex" v-show="show_error"> <small style="color: red; margin-right: auto;" > $[this.error_message]$ </small> </div> </div> </form> </div> <ul class="navbar-nav"> <!-- explore dropdown --> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle text-nowrap" href="#" id="navbarDropdown" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">Explore <span class="caret"></span></a> <div class="dropdown-menu" role="menu"> <a class="dropdown-item" href="/oma/release/">Species/release information</a> <a class="dropdown-item" href="/oma/phylostratigraphy/">Phylostratigraphy</a> <div class="dropdown-divider"></div> <div role="presentation" class="dropdown-header">Quick access to</div> <a class="dropdown-item" href="/oma/genome/">Extant and Ancestral genomes</a> <a class="dropdown-item" href="/oma/landOMA/">OMA groups</a> <a class="dropdown-item" href="/oma/hogs/">Hierarchical orthologous groups (HOGs)</a> <a class="dropdown-item" href="/oma/landAnnotation/">Functional annotations</a> <a class="dropdown-item" href="/oma/synteny/">Local synteny</a> </div> </li> <!-- compute dropdown --> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle text-nowrap" data-toggle="dropdown">Tools <span class="caret"></span></a> <div class="dropdown-menu" role="menu"> <div role="presentation" class="dropdown-header">Online tools</div> <a class="dropdown-item" href="/oma/fastmapping/">Fast mapping</a> <a class="dropdown-item" href="/oma/functions/">Functional prediction</a> <a class="dropdown-item" href="/oma/dotplot/">Synteny dotplot</a> <a class="dropdown-item" href="/oma/genomePW/">Genome pair orthology</a> <a class="dropdown-item" href="/oma/go_enrichment/">GO enrichment analysis</a> <a class="dropdown-item" href="/oma/omamo/search/">OMA-MO: Find model organism</a> <a class="dropdown-item" href="https://omark.omabrowser.org">OMArk: Assess proteome quality</a> <div class="dropdown-divider"></div> <div role="presentation" class="dropdown-header">Software</div> <a class="dropdown-item" href="https://omabrowser.org/standalone/">OMA StandAlone</a> <a class="dropdown-item" href="https://github.com/dessimozlab/read2tree">read2tree</a> <a class="dropdown-item" href="https://github.com/dessimozlab/FastOMA">FastOMA</a> <a class="dropdown-item" href="https://github.com/dessimozlab/pyham">pyHam</a> <div class="dropdown-divider"></div> <div role="presentation" class="dropdown-header">Visualisation tools</div> <a class="dropdown-item" href="https://phylo.io/">Phylo.io</a> <a class="dropdown-item" href="https://github.com/dessimozlab/iham">IHam</a> <div class="dropdown-divider"></div> <a class="dropdown-item text-center" href="/oma/tools/"><b> <i class="fas fa-toolbox"></i> See all OMA tools</b></a> </div> </li> <!-- Download dropdown --> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle text-nowrap" data-toggle="dropdown">Download <span class="caret"></span></a> <ul class="dropdown-menu" role="menu"> <div role="presentation" class="dropdown-header">OMA database files</div> <a class="dropdown-item" href="/oma/current/">Current release</a> <a class="dropdown-item" href="/oma/export/">Export All/All</a> <a class="dropdown-item" href="/oma/export_markers">Export marker genes</a> <a class="dropdown-item" href="/oma/archives/">Archives</a> <div class="dropdown-divider"></div> <div role="presentation" class="dropdown-header">API</div> <a class="dropdown-item" href="/api/docs">OMA API</a> <a class="dropdown-item" href="/oma/APISOAP/">SOAP</a> <a class="dropdown-item" href="https://bioconductor.org/packages/release/bioc/html/OmaDB.html">R API binding</a> <a class="dropdown-item" href="https://github.com/DessimozLab/pyomadb">Python API binding</a> <div class="dropdown-divider"></div> <div role="presentation" class="dropdown-header">Semantic web</div> <a class="dropdown-item" href="https://sparql.omabrowser.org/">SPARQL endpoint</a> <div class="dropdown-divider"></div> <a class="dropdown-item text-center" href="/oma/uses/"><b> <i class="fas fa-keyboard"></i> Access the OMA data</b></a> </ul> </li> <!-- Help dropdown --> <li class="nav-item dropdown"> <a href="#" class="nav-link dropdown-toggle text-nowrap" data-toggle="dropdown">Help <span class="caret"></span></a> <ul class="dropdown-menu dropdown-menu-right" role="menu"> <a class="dropdown-item" href="/oma/about/">Introduction</a> <a class="dropdown-item" href="/oma/type/">Orthology Basics</a> <a class="dropdown-item" href="/oma/homologs/">Type of homologs</a> <a class="dropdown-item" href="/oma/uses/">Access the OMA data</a> <a class="dropdown-item" href="/oma/tools/">Catalog of tools</a> <a class="dropdown-item" href="/oma/suggestion/genome/">Suggesting a genome</a> <a class="dropdown-item" href="/oma/FAQ/">FAQ</a> <a class="dropdown-item" href="https://www.biostars.org/tag/oma/">Q&A on BioStars</a> <a class="dropdown-item " href="/oma/glossary/"> Glossary</a> <div class="dropdown-divider"></div> <a class="dropdown-item text-center" href="/oma/academy/"><b> <i class="fas fa-book"></i> OMA Academy</b></a> </ul> </li> <!-- about dropdown --> <li class="nav-item dropdown"> <a class="nav-link dropdown-toggle text-nowrap" href="#" role="button" data-toggle="dropdown" aria-haspopup="true" aria-expanded="false">About <span class="caret"></span></a> <div class="dropdown-menu dropdown-menu-right" role="menu"> <a class="dropdown-item" href="/oma/about/">OMA</a> <a class="dropdown-item" href="/oma/team/">Team</a> <a class="dropdown-item" href="/oma/sab/">SAB</a> <a class="dropdown-item" href="/oma/funding/">Funding</a> <a class="dropdown-item" href="/oma/terms_of_use/">Terms of use</a> <div class="dropdown-divider"></div> <a class="dropdown-item" href="mailto:contact@omabrowser.org"><span class="glyphicon glyphicon-envelope"></span> Contact</a> </div> </li> </ul> </div> </div> </nav> <div id="oma-generic-container"> <div class="container"> <div class="jumbotron"> <h1>OMA in a nutshell (Introduction) <span> <small class="text-center text-muted h3 d-block">Web based database interface for orthology prediction </small></span></h1> <div class="oma-seperator"> <span class="colour1"></span> <span class="colour2"></span> <span class="colour3"></span> </div> <div class="card card-header-oma border-0"> <h2> Why OMA? </h2> <hr> <div class="card-body"> <p class="text-justify">The OMA (“Orthologous MAtrix”) project is a method and database for the inference of orthologs among complete genomes. </p> <p class="text-justify"> The distinctive features of OMA are its: <ul> <li> Broad scope and size </li> <li> <a id='linkToBench' href='#bench'>High quality of inferences</a> </li> <li>Feature-rich web interface </li> <li><a href="/oma/current/"> Availability of data in a wide range of formats and interfaces </a> </li> <li>Frequent update schedule of two releases per year </li> </ul> <p class="text-justify"> The OMA pipeline can also run on custom genomic/transcriptomic data using the OMA stand-alone software, and it is even possible to combine precomputed data with custom data by exporting parts of the OMA database. </p> </div> </div> <br> <div class="card card-header-oma border-0"> <h2>History</h2> <hr> <div class="card-body"> <p class="lead"></p> <p class="text-justify">The OMA project was initiated in 2004 at ETH Zurich by Prof. Gaston Gonnet, with the goal of identifying orthologs among all publicly available genomes. At the time, most sequenced genomes were bacteria and only few were eukaryotes. Several PhD students in his group became increasingly involved, in particular Adrian Schneider, Christophe Dessimoz, and Alexander Roth. Over the subsequent 15 years, OMA underwent 24 major releases, steadily increasing the number of genomes under consideration. </p> <img src="/static/image/history.png" class="rounded mx-auto d-block w-50 p-3 " alt="Graph showing growth of OMA over time."> <div class="text-center small"> <b> Graph showing growth of OMA over time.</b> </div> <br> <p class="text-justify">The OMA Browser was introduced in 2006. Early releases were developed by Adrian Schneider and Christophe Dessimoz. Adrian Altenhoff joined the team in 2008. </p> <p class="text-justify">In 2008, the responsibility of “baby-sitting” the all-against-all (i.e. importing and converting genomes, running and verifying computations across hundreds of CPUs) was handed over from Gaston to the two Adrians.</p> <p class="text-justify">Since 2010, Adrian Altenhoff has been the main baby-sitter of the all-against-all and manager of OMA’s operations. In 2011, Christophe joined Gaston as co-PI of OMA. In 2012, OMA became a SIB-funded bioinformatics resource.</p> </div> </div> <div class="card card-header-oma border-0"> <h2>The OMA algorithm</h2> <hr> <div class="card-body"> <p class="text-justify">OMA’s inference algorithm consists of three main phases. First, to infer homologous sequences (sequences of common ancestry), <a href="/oma/glossary/#g-allall" >all-against-all </a> Smith-Waterman alignments are computed and significant matches are retained. Second, to infer <a href="/oma/glossary/#g-op" >orthologous pairs </a> (the subset of homologs related by speciation events), mutually closest homologs are identified based on <a href="/oma/glossary/#g-evod" >evolutionary distances </a> , taking into account distance inference uncertainty and the possibility for differential gene losses (for more details, see <a href="http://www.biomedcentral.com/1471-2105/10/220">Roth et al 2008</a>). Third, these orthologs are clustered in two different ways, which are useful for different purposes: <ul> <li> We identify cliques of orthologous pairs (<a href="/oma/glossary/#g-og" >“OMA groups” </a> ), which are useful as <a href="/oma/glossary/#g-markerg" >marker genes </a> for phylogenetic reconstruction and tend to be very specific; </li> <li>We identify <a href="/oma/glossary/#g-hog" >hierarchical orthologous groups </a> (“HOGs”), groups of genes defined for particular <a href="/oma/glossary/#g-taxr" >taxonomic ranges </a> and identify all genes that have descended from a common ancestral gene in that taxonomic range. </li> </ul> <h4> More details on the algorithm </h4> <ul> <li> How to Identify Orthologs with OMA: A Primer <a href="https://f1000research.com/articles/9-27/v1">(Zahn-Zabal et al. 2020)</a></li> <li>Inferring HOGs <a href="http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0053786"">(Altenhoff et al. 2013)</a></li> <li>Updates to the OMA algorithm <a href="">(Train et al. 2017)</a></li> <li>Initial OMA algorithm <a href="">(Roth et al. 2008)</a></li> </ul> <p class="text-justify"> For more info on the features of the OMA Browser, please consult the help pages accessible from the navigation bar in the top-right corner. </p> </div> </div> <br> <div class="card card-header-oma border-0"> <h2>Publications</h2> <hr> <div class="card-body"> <h4 id='publications' class="panel-heading">OMA overview</h4> <p class="text-justify">Adrian M Altenhoff, Alex Warwick Vesztrocy, Charles Bernard, Clement-Marie Train, Alina Nicheperovich, Silvia Prieto Baños, Irene Julca, David Moi, Yannis Nevers, Sina Majidian, Christophe Dessimoz, Natasha M Glover<br/> <em>OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem</em><br/> Nucleic Acids Research, 2024, <b>52</b>(D1):D513–D521 <a href="https://doi.org/10.1093/nar/gkad1020">Full text</a> </p><br/> <p class="text-justify">Adrian M Altenhoff, Clément-Marie Train, Kimberly J Gilbert, Ishita Mediratta, Tarcisio Mendes de Farias, David Moi, Yannis Nevers, Hale-Seda Radoykova, Victor Rossier, Alex Warwick Vesztrocy, Natasha M Glover, Christophe Dessimoz<br/> <em>OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more</em><br/> Nucleic Acids Research, 2021, <b>49</b>(D1):D373–D379 <a href="https://doi.org/10.1093/nar/gkaa1007">Full text</a> </p><br/> <p class="text-justify">Adrian M Altenhoff, Natasha M Glover, Clément-Marie Train, Klara Kaleb, Alex Warwick Vesztrocy, David Dylus, Tarcisio Mendes de Farias, Karina Zile, Charles Stevenson, Jiao Long, Henning Redestig, Gaston H Gonnet and Christophe Dessimoz<br> <em>The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces</em><br> Nucleic Acids Research, 2018, <b>46</b>(D1): D477-D485 <a href="https://doi.org/10.1093/nar/gkx1019">Full text</a></p> <br> <p class="text-justify">Adrian M. Altenhoff, Nives Škunca, Natasha Glover, Clément-Marie Train, Anna Sueki, Ivana Piližota, Kevin Gori, Bartlomiej Tomiczek, Steven Müller, Henning Redestig, Gaston H Gonnet and Christophe Dessimoz<br> <em> The OMA orthology database in 2015: function predictions, better plant support, synteny view, and other improvements </em><br> Nucleic Acids Research, 2015, <b>43</b>(D1): D240-D249 <a href="https://dx.doi.org/10.1093/nar/gku1158"> Full text</a> </p> <br> <p class="text-justify">Adrian M. Altenhoff, Adrian Schneider, Gaston H. Gonnet, Christophe Dessimoz <br> <em> OMA 2011: Orthology Inference Among 1,000 Complete Genomes </em><br> Nucleic Acids Research, 2011, 39 (suppl 1): D289-D294 <a href='https://nar.oxfordjournals.org/content/39/suppl_1/D289'> Full text</a> </p> <br> <p class="text-justify">Adrian Schneider, Christophe Dessimoz, Gaston H. Gonnet <br> <em> OMA Browser - Exploring orthologous relations across 352 complete genomes </em><br> Bioinformatics, 2007, 23:16 (pp. 2180-2182) <a href="/">Project page </a> <a href='http://bioinformatics.oxfordjournals.org/content/23/16/2180'> Full text </a> </p> <br> <h3>OMA algorithm</h3> <br> <p class="text-justify">Natasha M. Glover, Adrian Altenhoff, Christophe Dessimoz<br> <em>Assigning confidence scores to homoeologs using fuzzy logic</em> PeerJ, 2019, 6, e6231 doi: 10.7717/peerj.6231 <a href="https://dx.doi.org/10.7717/peerj.6231">Full text</a> </p> <br> <p>Clément-Marie Train, Natasha M. Glover, Gaston H. Gonnet, Adrian M. Altenhoff, Christophe Dessimoz<br> <em>Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference</em><br> Bioinformatics, 2017, 33:14, (pp. i75–i82) <a href="https://doi.org/10.1093/bioinformatics/btx229">Full text</a> </p> <br> <p class="text-justify">Adrian M. Altenhoff, Manuel Gil, Gaston H. Gonnet, Christophe Dessimoz <br> <em> Inferring Hierarchical Orthologous Groups From Orthologous Gene Pairs </em><br> PLoS One, 2013, 8:1, e53786 <a href="https://omabrowser.org/standalone/">Software </a> <a href='http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0053786'> Full text </a> </p> <br> <p class="text-justify">Alexander Roth, Gaston H. Gonnet, Christophe Dessimoz <br> <em> Algorithm of OMA for Large-Scale Orthology Inference </em><br> BMC Bioinformatics, 2008, 9:518 <a href='http://www.biomedcentral.com/1471-2105/9/518'> Full text</a> <a href="http://www.biomedcentral.com/1471-2105/10/220">(Please note the associated erratum) </a> </p> <br> <p class="text-justify">Christophe Dessimoz, Brigitte Boeckmann, Alexander Roth, Gaston H. Gonnet <br> <em> Detecting Non-Orthology in the COGs Database and Other Approaches Grouping Orthologs Using Genome-Specific Best Hits </em><br> Nucleic Acids Res, 2006 34:11 (pp. 3309-3316) <a href='http://nar.oxfordjournals.org/content/34/11/3309'> Full text </a> </p> <br> <p class="text-justify">Christophe Dessimoz, Gina Cannarozzi, Manuel Gil, Daniel Margadant, Alexander Roth, Adrian Schneider, Gaston H. Gonnet <br> <em> OMA, a Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements </em><br> RECOMB 2005 Workshop on Comparative Genomics, LNCS 3678 (pp. 61-72) <a href='http://download.springer.com/static/pdf/65/chp%253A10.1007%252F11554714_6.pdf?auth66=1408719784_5261138a05efa9237079a02f2783af34&ext=.pdf'> Full text </a> <a href='http://link.springer.com/chapter/10.1007%2F11554714_6'> Abstract </a> </p> <br> <h3 id='bench'>Benchmarking</h3> <br> <p class="text-justify">Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium, Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.<br> <em> Standardized benchmarking in the quest for orthologs </em><br> Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830 <a href="http://dx.doi.org/10.1038/nmeth.3830">Full text</a> </p> <br> <p class="text-justify">Daniel A. Dalquen, Adrian M. Altenhoff, Gaston H. Gonnet, Christophe Dessimoz <br> <em> The Impact of Gene Duplication, Insertion, Deletion, Lateral Gene Transfer and Sequencing Error on Orthology Inference: a Simulation Study </em><br> PLoS One, 2013, 8:2, e56925 <a href='http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0056925'> Full text </a> </p> <br> <p class="text-justify">Brigitte Boeckmann, Marc Robinson-Rechavi, Ioannis Xenarios, Christophe Dessimoz <br> <em> Conceptual Framework and Pilot Study to Benchmark Phylogenomic Databases Based on Reference Gene Trees </em><br> Briefings in Bioinformatics, 2011, 12:5 (pp. 474-484) <a href='http://bib.oxfordjournals.org/content/12/5/423'> Full text </a> </p> <br> <p class="text-justify">Adrian M. Altenhoff and Christophe Dessimoz<br> <em>Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods </em><br> PLoS Computational Biology, 2009, 5:1, e1000262 <a href='http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1000262'> Full text </a> </p> <br> <h3>Orthology inference in general</h3> <br> <p class="test-justify">Adrian M. Altenhoff, Natasha M. Glover, and Christophe Dessimoz<br> <em>Inferring Orthology and Paralogy.</em> In: Evolutionary Genomics. Statistical and Computational methods <em>(M Anisimova, Editor)</em> Methods in Molecular Biology, 2019, Springer Humana, Vol 1910. <a href="https://doi.org/10.1007/978-1-4939-9074-0_5"> Full text</a> </p> </div> </div> <br> <div class="card card-header-oma border-0"> <h2>Related Resources</h2> <hr> <div class="card-body"> <a href="https://swissorthology.ch"><img style="max-width: 200px;" src="/static/image/logo-swiss-orthology.svg"></a> <p class="text-justify">The OMA Browser is part of the <a href="https://swissorthology.ch">SwissOrthology</a> initiative. SwissOrthology combines a number of Swiss web-resources that are centered around orthology and are funded by <a href="https://sib.swiss">SIB</a>.</p> </div> </div> </div> </div> </div> </body> </html>