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class="mainMenu__greenText m-l-1"></span></a> </li> </ul> </nav> </div> </div> </div> <div id="site-wrapper" class="site-wrapper"> <div feedback data-nosnippet></div> <div notifications data-nosnippet></div> <div user-menu data-nosnippet></div> <div menu-search data-nosnippet></div> <div language-menu data-nosnippet></div> <main id="main" class="main" role="main" ui-view> <div class="site-content"> <div class="site-content__page"> <div> <article class="wrapper-horizontal-stripes speciesLookup page--data" ng-controller="sequenceMatchingCtrl as vm"> <div class="speciesLookup__overlay ng-cloak" ng-show="vm.download"> <div class="speciesLookup__overlay__card"> <div class="speciesLookup__overlay__card__header"> <h4>Download as .csv</h4> </div> <div class="speciesLookup__overlay__card__download seperator--b seperator"> <div> <a id="sequenceMatcher_generatedCsv" href="" download='blastresult.csv' ng-click="vm.download = false" class="gb-icon-cloud-download"></a> </div> </div> <div class="site-drawer__bar"> <a href="" class="site-drawer__bar__action" ng-click="vm.download = false"> <span>cancel</span> </a> </div> </div> </div> <a href="" class="speciesLookup__back" onclick="location.reload();return false;"><span class="h1 gb-icon-left-arrow"></span></a> <div class="horizontal-stripe article-header white-background"> <div class="row"> <div class="col-xs-12"> <nav class="article-header__category article-header__category--deep"> <span class="article-header__category__upper" >Tools</span> <span class="article-header__category__lower" >Sequence ID</span> </nav> </div> </div> </div> <div id="tabsScrollable"> <div class="horizontal-stripe--paddingless white-background seperator--b"> <div class="container--desktop" ng-class="{'nameParser__tabs-container' : !vm.species}"> <div class="tabs__wrapper"> <div class="tabs tabs--noBorder"> <ul class="anchorTabs"> <li class="tab" ng-class="{isActive: vm.$location.path().indexOf('/about') === -1}"> <a ng-href="/tools/sequence-id" > Sequence ID </a> </li> <li class="tab" ng-class="{isActive: vm.$location.path().indexOf('/about') !== -1}"> <a ng-href="/tools/sequence-id/about"> <span translate="nameParser.about"> About </span> </a> </li> </ul> </div> </div> </div> </div> </div> <ng-include src="'/templates/sequence-matching/about.html?locale='+vm.locale" ng-if="vm.$location.path().indexOf('/about') > -1"></ng-include> <div ng-if="vm.$location.path().indexOf('/about') === -1">  <div ng-if="!vm.species" class="light-background"> <div layout="row" layout-align="center start" ng-cloak> <div class="nameParser__prose" > <p>This tool will query taxonomy reference databases for Fungi, Animals, Bacteria and Archaea</p> <ul class="sequenceMatcher__list m-b-05"> <li><strong>ITS</strong> sequences for Fungi will be queried against the <a href="https://unite.ut.ee/repository.php">UNITE general FASTA release for eukaryotes v9.0</a> (a reference database for DNA barcoding of Fungi)</li> <li><strong>COI</strong> sequences for Animals will be queried against a 99% clustered version of the <a href="https://doi.org/10.15468/inygc6">BOLD Public Database v2024-07-19</a> public data (COI-5P sequences)</li> <li><strong>16S</strong> sequences for Bacteria and Archaea will be queried against the <a href="https://gtdb.ecogenomic.org/downloads">Genome Taxonomy Database r214</a> 16S rRNA gene sequences identified within the set of representative genomes</li> <li><strong>18S</strong> sequences will be queried against the <a href="https://pr2-database.org//">PR2 database</a> v5.0.0</li> <li><strong>12S</strong> sequences for Fish will be queried against the <a href="http://mitofish.aori.u-tokyo.ac.jp/">MitoFish</a> v3.97 database of 12S sequences</li> </ul> <p>Files can be uploaded in CSV or FASTA format. CSVs are expected to have a columns named 'sequence', 'marker' and an 'id' or 'occurrenceId' column. It is also possible to paste sequences into the text field below (only FASTA format)</p> </div> </div> <div layout="row" layout-align="center start" layout-padding ng-cloak> <div class="nameParser__name-paste-form" layout-align="start center"> <form > <label >Select marker</label> <md-radio-group ng-model="vm.selectedMarker" layout="row"> <md-radio-button class="md-primary" value="ITS" >ITS</md-radio-button> <md-radio-button class="md-primary" value="COI"> COI </md-radio-button> <md-radio-button class="md-primary" value="16S"> 16S </md-radio-button> <md-radio-button class="md-primary" value="18S"> 18S </md-radio-button> <md-radio-button class="md-primary" value="12S"> 12S </md-radio-button> </md-radio-group> <md-input-container class="md-block "> <label >Paste sequences here (fasta format, remember to select marker)</label> <textarea class="nameParser__name-paste-area" ng-model="vm.inputList" rows="10" md-select-on-focus></textarea> </md-input-container> <div class="text-center"> <button class="gb-button--primary nameParser__parse-button" ng-click="vm.loadTestData()" > Load test data </button> <button class="gb-button--primary nameParser__parse-button" ng-click="vm.handleFasta(vm.inputList)" >Blast </button></div> </form> </div> <div> <div layout="column" layout-align="center center"> <div class="nameParser__input-file"> <input type="file" onchange="angular.element(this).scope().handleFiles(this.files)"/> <a href="" translate="nameParser.selectFile">Select file</a> </div> <p class="ng-cloak" translate="nameParser.or">or</p> </div> <p class="speciesLookup__dropArea ng-cloak text-uppercase" droppable drop="vm.handleDrop">{{'nameParser.dropHere' | translate}}</p>   <div class="text-center m-t-2 ng-cloak" ng-if="vm.error"> <p>Cannot read file</p> <span class="badge badge--error ng-cloak">{{ vm.error }}</span> </div> </div> </div> <div layout="row" layout-align="center start" ng-cloak> <div class="nameParser__prose"> <h4>References</h4> <div layout="row" > <div class="small p-r-1" flex="33"> <div> UNITE Community (2022):UNITE general FASTA release for eukaryotes 2. Version 2022-11-29. UNITE Community. </div> <doi link="https://doi.org/10.15156/BIO/786353"></doi> </div> <div class="small p-r-1" flex="33"> <div> Nilsson, R.H. et.al. (2019). The UNITE database for molecular identification of fungi: handling dark taxa and parallel taxonomic classifications. Nucleic Acids Research. Volume 47, Issue D1, Pages D259–D264 </div> <doi link="https://doi.org/10.1093/nar/gky1022"></doi> </div> <div class="small p-r-1" flex="33"> <div> Sato Y, Miya M, Fukunaga T, Sado T, Iwasaki W. 2018. MitoFish and MiFish Pipeline: A Mitochondrial Genome Database of Fish with an Analysis Pipeline for Environmental DNA Metabarcoding. Mol Biol Evol 35:1553-1555. </div> <doi link="https://doi.org/10.1093/molbev/msy074"></doi> </div> </div> <div layout="row" class="m-t-1 m-b-1" > <div class="small p-r-1" flex="33"> <div> Ratnasingham, S., & Hebert, P. D. N. (2013, July 8). A DNA-Based Registry for All Animal Species: The Barcode Index Number (BIN) System. (D. Fontaneto, Ed.) PLoS ONE. Public Library of Science (PLoS). </div> <doi link="http://doi.org/10.1371/journal.pone.0066213"></doi> </div> <div class="small p-r-1" flex="33"> <div> The International Barcode of Life Consortium (2016). International Barcode of Life project (iBOL). Occurrence dataset accessed via GBIF.org on 2023-03-12. </div> <doi link="https://doi.org/10.15468/inygc6"></doi> </div> <div class="small p-r-1" flex="33"> <div> Guillou, L., Bachar, D., Audic, S., Bass, D., Berney, C., Bittner, L., Boutte, C. et al. 2013. The Protist Ribosomal Reference database (PR2): a catalog of unicellular eukaryote Small Sub-Unit rRNA sequences with curated taxonomy. Nucleic Acids Res. 41:D597–604. </div> <doi link="https://doi.org/10.1093/nar/gks1160"></doi> </div> </div> <div layout="row" class="m-t-1 m-b-1" > <div class="small p-r-1" flex="33"> <div> Parks DH., Chuvochina M, Chaumeil P, Rinke C, Mussig AJ, Hugenholtz P (2020). A complete domain-to-species taxonomy for Bacteria and Archaea. Nature Biotechnology volume 38, pages 1079–1086 </div> <doi link="https://doi.org/10.1038/s41587-020-0501-8"></doi> </div> <div class="small p-r-1" flex="33"> <div> Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A, Chaumeil P, Hugenholtz P (2018). A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nature Biotechnology volume 36, pages 996–1004 </div> <doi link="https://doi.org/10.1038/nbt.4229"></doi> </div> <div class="small p-r-1" flex="33"> <div> Daniel Vaulot, Javier del Campo, Mahwash Jamy, Fabien Burki, Laure Guillou, Luciana Santoferrara, Maximilian Ganser, Andrea de Oliveira da Rocha Franco, Kenneth Mertens, Haifeng Gu, Se Hyeon Jang, Pavel Škaloud, Manon Dünn, Megan Gross, Алексей Селюк, Miguel Mendez Sandin, Sebastian Metz, Richard Dorrell, & AnnaMaria Fiore-Donno. (2023). pr2database/pr2database: PR2 version 5.0.0 (v5.0.0). Zenodo. </div> <doi link="https://doi.org/10.5281/zenodo.7805244"></doi> </div> </div> </div> </div> </div> <section class="horizontal-stripe light-background seperator--b" ng-if="vm.species.length && !vm.error"> <div class="container--desktop"> <div class="row"> <div class="col-xs-12"> <div class="container-fluid card" ng-cloak ng-if="vm.lookupComplete"> <div class="row card__content"> <div class="col-xs-12"> <div ng-if="vm.selectedMarker === 'ITS'"> <p>Your data have been matched against a blast database of the <a href="https://unite.ut.ee/repository.php">UNITE general FASTA release for eukaryotes v9.0</a>. All returned matches have then been matched against the GBIF backbone taxonomy by their identifier (e.g. SH1571756.08FU). These OTU identifiers can be used for publishing sequence based data to GBIF. The result can be downloaded as a csv with identifiers included.</p> </div> <div ng-if="vm.selectedMarker === 'COI'"> <p>Your data have been matched against a 99% clustered version of the <a href="https://doi.org/10.15468/inygc6">BOLD Public Database v2024-07-19</a> public data (COI-5P sequences) All returned matches have then been matched against the GBIF backbone taxonomy by their identifier (e.g. BOLD:ADJ8357). These OTU identifiers can be used for publishing sequence based data to GBIF. The result can be downloaded as a csv with identifiers included.</p> </div> <div ng-if="vm.selectedMarker === '16S'"> <p>Your data have been matched against the <a href="https://gtdb.ecogenomic.org/downloads">Genome Taxonomy Database r214</a> 16S rRNA gene sequences identified within the set of representative genomes</p> </div> <div ng-if="vm.selectedMarker === '12S'"> <p>Your data have been matched against the <a href="http://mitofish.aori.u-tokyo.ac.jp/">MitoFish</a> v3.97 database of 12S sequences</p> </div> <div ng-if="vm.selectedMarker === '18S'"> <p>Your data have been matched against the <a href="https://pr2-database.org/">PR2</a> v5.0.0 database of 18S sequences</p> </div>  </div> <div class="col-xs-12"> <h4>Match types</h4> <table class="table sequenceMatcher__summaryTable" > <tbody> <tr > <td ><span ng-class="vm.getMatchTypeClass('BLAST_EXACT_MATCH')">{{ 'BLAST_EXACT_MATCH' | prettifyEnum }}</span></td> <td > identity >= 99% and queryCoverage >= 80%. This is within the threshold of the OTU. </td> </tr> <tr > <td ><span ng-class="vm.getMatchTypeClass('BLAST_AMBIGUOUS_MATCH')">{{ 'BLAST_AMBIGUOUS_MATCH' | prettifyEnum }}</span></td> <td > {{'identity >= 99% and queryCoverage >= 80%, but there is at least one more match with similar identity'}} </td> </tr> <tr > <td ><span ng-class="vm.getMatchTypeClass('BLAST_CLOSE_MATCH')">{{ 'BLAST_CLOSE_MATCH' | prettifyEnum }}</span></td> <td > {{'identity < 99% but > 90% and queryCoverage >= 80%. It is something close to the OTU, maybe the same Genus.'}} </td> </tr> <tr > <td ><span ng-class="vm.getMatchTypeClass('BLAST_WEAK_MATCH')">{{ 'BLAST_WEAK_MATCH' | prettifyEnum }}</span></td> <td > {{'there is a match, but with identity < 90% or/and queryCoverage < 80%. Depending on the quality of the sequence, bit score, identity and expect value, a higher taxon could be inferred from this.'}} </td> </tr> <tr > <td ><span ng-class="vm.getMatchTypeClass('BLAST_NO_MATCH')">{{ 'BLAST_NO_MATCH' | prettifyEnum }}</span></td> <td > No match. </td> </tr> </tbody> </table> </div> </div> </div> <div class="card container-fluid"> <div class="row summaryStats" ng-if="vm.species.length" ng-cloak> <a class="col-xs-12 summaryStats__item" ng-if="!vm.lookupComplete"> <div> <div class="summaryStats__circle"> <round-progress max="100" current="( 100*vm.matchedSequenceCount / vm.species.length)" bgcolor="#dbefef" color="#71b171" responsive="true"> </round-progress> </div> <div class="summaryStats__percentage"> <span>{{ ( vm.matchedSequenceCount / vm.species.length) | formatAsPercentage:100 }}%</span> <div >{{vm.matchedSequenceCount}} of {{vm.species.length}} sequences processed</div> </div> </div> </a> <a class="col-xs-12 col-sm-6 col-md-3 summaryStats__item" ng-if="vm.lookupComplete"> <div> <div class="summaryStats__circle summaryStats__circle--occurrences"></div> <div class="summaryStats__percentage"> <span>{{ vm.species.length | localNumber }}</span> <div> sequences</div> </div> </div> </a> <a class="col-xs-12 col-sm-6 col-md-3 summaryStats__item" ng-if="vm.lookupComplete"> <div> <div class="summaryStats__circle"> <round-progress max="100" current="( 100*vm.blastMatchCount / vm.species.length)" bgcolor="#dbefef" color="#71b171" responsive="true"> </round-progress> </div> <div class="summaryStats__percentage"> <span>{{ ( vm.blastMatchCount / vm.species.length) | formatAsPercentage:100 }}%</span> <div >with blast match</div> </div> </div> </a> <a class="col-xs-12 col-sm-6 col-md-3 summaryStats__item" ng-if="vm.lookupComplete"> <div> <div class="summaryStats__circle"> <round-progress max="100" current="( 100*vm.aboveThresholdCount / vm.species.length)" bgcolor="#dbefef" color="#71b171" responsive="true"> </round-progress> </div> <div class="summaryStats__percentage"> <span>{{ ( vm.aboveThresholdCount / vm.species.length) | formatAsPercentage:100 }}%</span> <div >with identity > {{vm.matchThreshold}}%</div> </div> </div> </a> <a class="col-xs-12 col-sm-6 col-md-3 summaryStats__item" ng-if="vm.lookupComplete"> <div> <div class="summaryStats__circle"> <round-progress max="100" current="( 100*vm.inBackboneCount / vm.species.length)" bgcolor="#dbefef" color="#71b171" responsive="true"> </round-progress> </div> <div class="summaryStats__percentage"> <span>{{ ( vm.inBackboneCount / vm.species.length) | formatAsPercentage:100 }}%</span> <div >with GBIF backbone match</div> </div> </div> </a> </div> </div> </div> </div> <div class="card m-t-1" ng-if="vm.matchError"> <div class="card__content card__content--warning" > <p ng-bind="vm.matchError"></p> </div> </div> </div> </section>  <div class="horizontal-stripe--paddingless white-background nameParser__result-table ng-cloak" ng-if="vm.species && vm.processing && !vm.error"> <div class="occurrence-search__table__area"> <div class="scrollable-y"> <div class="table-container"> {{ species }} <table class="table search-table"> <thead> <tr> <th ng-repeat="col in ['occurrenceId', 'marker', 'identity', 'bitScore', 'expectValue', 'queryCoverage', 'queryLength', 'matchType', 'scientificName', 'alignment','classification', 'sequence']"> <a href="" ng-click="vm.state.sortType = col; vm.state.sortReverse = !vm.state.sortReverse"> <span class="inline-block"> {{ col }} <span ng-show="vm.state.sortType == col && !vm.state.sortReverse" class="sortReverse">▲</span> <span ng-show="vm.state.sortType == col && vm.state.sortReverse" class="sortReverse">▼</span> </span> <span ng-if="vm.help[col]" gb-help="{{vm.help[col]}}" gb-help-options="{isCms: false}" ng-click="$event.stopPropagation();"></span> </a> </th> </tr> </thead> <tbody> <tr ng-repeat="species in vm.species | orderBy:vm.state.sortType:vm.state.sortReverse | startFrom:vm.pagination.currentPage*vm.pagination.pageSize-vm.pagination.pageSize | limitTo:vm.pagination.pageSize"> <td class="table-cell"> <span>{{ species.occurrenceId }}</span> </td> <td class="table-cell--narrow"> <span>{{ species.marker }}</span> </td> <td class="table-cell--narrow"> <span ng-if="species.identity">{{ species.identity }}%</span> </td> <td class="table-cell--narrow"> <span>{{ species.bitScore }}</span> </td> <td class="table-cell--narrow"> <span>{{ species.expectValue }}</span> </td> <td class="table-cell--narrow"> <span ng-if="species.queryCoverage">{{ species.queryCoverage }}%</span> </td> <td class="table-cell--narrow"> <span>{{ species.queryLength }}</span> </td> <td class="table-cell"> <span ng-class="vm.getMatchTypeClass(species.matchType)">{{ species.matchType | prettifyEnum }}</span> </td> <td class="table-cell--widder" > <div style="width: 30em" layout="row" layout-align="space-between center"> <a ng-if="species.nubMatch && species.nubMatch.usage" ng-href="/species/{{species.nubMatch.usage.key}}" ng-bind-html="species.nubMatch.usage.formattedName" target="_BLANK"></a> <span ng-if="!(species.nubMatch && species.nubMatch.usage) && species.matchType && species.matchType !== 'BLAST_NO_MATCH'">{{species.scientificName}} <a class="gb-icon-link" ng-if="species.marker.toLowerCase().indexOf('its') > -1" ng-href="https://dx.doi.org/10.15156/BIO/{{species.scientificName}}" target="_blank"></a> <a class="gb-icon-link" ng-if="species.marker.toLowerCase().indexOf('coi') > -1 || species.marker.toLowerCase().indexOf('co1') > -1" ng-href="http://bins.boldsystems.org/index.php/Public_BarcodeCluster?clusteruri={{species.scientificName}}" target="_blank"></a> <a class="gb-icon-link" ng-if="species.marker.toLowerCase().indexOf('16s') > -1" ng-href="https://gtdb.ecogenomic.org/tree?r=s__{{species.scientificName}}" target="_blank"></a> <a class="gb-icon-link" ng-if="species.marker.toLowerCase().indexOf('12s') > -1" ng-href="http://mitofish.aori.u-tokyo.ac.jp/species/detail/?genus={{species.scientificName.split(' ')[0]}}&species={{species.scientificName.split(' ')[1]}}" target="_blank"></a> <a class="gb-icon-link" ng-if="species.marker.toLowerCase().indexOf('18s') > -1" ng-href="https://www.ncbi.nlm.nih.gov/nuccore/{{species.accession}}" target="_blank"></a> <span class="discreet" ng-if="species.matchType !== 'BLAST_NO_MATCH'">(not in GBIF taxonomy)</span></span> <div ng-if="species.nubMatch && species.nubMatch.usage" class="hideInvalid" taxon-occ-img="{{ species.nubMatch.usage.key }}" ></div> </div> </td> <td> <button class="gb-button--primary nameParser__parse-button" ng-if="species.match" ng-click="vm.showAlignment(species.match)" >{{'Alignment'}} </button> </td> <td class="table-cell--widder"> <span ng-bind-html="species.formattedClassification"></span> </td> <td class="table-cell" style="min-width:20em">  <sequence seq="{{ species.sequence }}" limit="50"></sequence> </td> </tr> </tbody> </table> </div> </div> </div> <div class="container-fluid"> <div class="row"> <div class="col-xs-12 col-sm-6"> <div> <uib-pagination total-items="vm.species.length" ng-model="vm.pagination.currentPage" max-size="5" items-per-page="vm.pagination.pageSize" class="pagination-sm" boundary-link-numbers="true" rotate="true" ng-change="vm.pageChanged()" ng-show="vm.species.length > vm.pagination.pageSize"> </uib-pagination> </div> </div> <div class="col-xs-12 col-sm-6"> <div class="clearfix"> <div class="switch-group pull-right"> <p>Exclude unmatched</p> <input id="speciesLookupDiscardInCsv" type="checkbox" ng-model="vm.exclude" aria-label="Discard"/> <label for="speciesLookupDiscardInCsv" class="switch"></label> </div> </div> <div class="speciesLookup__generate" ng-if="vm.lookupComplete"> <a href="" ng-click="vm.generateCsv()" class="text-uppercase pull-right">generate CSV</a> </div> <div ng-if="!vm.lookupComplete" class="pull-right discreet"> Blasting sequences - hang on </div> </div> </div> </div> </div> <span class="gbHelp"> <div ng-cloak class="gbHelp__overlay" ng-if="vm.showAligmentOverlay"> <div class="gbHelp__content"> <div class="card gbHelp__card--loaded " > <div class="card__content" > <h3 ng-bind-html="vm.currentAligment.header"></h3> <span class="discreet" ng-bind-html="vm.currentAligment.subHeader"></span> <pre class="sequenceMatcher__alignment" ng-bind-html="vm.currentAligment.alignment"></pre> <div ng-if="vm.currentAligment.alternatives && vm.currentAligment.alternatives.length"> <h3>Alternatives:</h3> <div ng-repeat="alt in vm.currentAligment.alternatives"> <h4 ng-bind-html="alt.header"></h4> <span class="discreet" ng-bind-html="alt.subHeader"></span> <pre class="sequenceMatcher__alignment" ng-bind-html="alt.alignment"></pre> </div> </div> </div> </div> </div> <div class="gbHelp__close" ng-click="vm.closeAligmentOverlay()"></div> </div> </span> <div class="emptyInfo" ng-if="vm.error"> <h3 ng-bind="vm.error"></h3> </div> </div> </article> </div> </div> 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