Helicobacter pylori Genome Databases

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Sequence search and alignment.</h3> <p style="line-height: 0.7em"> <a href="http://biocyc.org/PToolsWebsiteHowto.shtml#celOverview" class="learn-more-href">Learn More</a> </p> </div> <div class="slidePic"> <picture> <source srcset="/dispatchImages/BioCyc-Tools-Image-w582.webp" type="image/webp" media="(min-width: 800px)"> <source srcset="/dispatchImages/BioCyc-Tools-Image-w285.webp" type="image/webp"> <source srcset="/dispatchImages/BioCyc-Tools-Image-w285.png" media="(min-width: 799px)"> <img class="pure-img" src="/dispatchImages/BioCyc-Tools-Image-w582.png" alt="Collage of BioCyc Tools" width="582px" height="282px"> </picture> <p class="caption">&nbsp</p> </div> </div> <div class="slide"> <div class="slideText"> <h2 class="whitespace-none" style="font-size: 1.5em; padding-top: 10px;">Explore Metabolic Maps for Thousands of Organisms</h2> <h3 class="subhead"> The Cellular Overview enables you to browse through zoomable metabolic map diagrams that are customized to each BioCyc organism. </h3> <p style="line-height: 0.7em"> <a href="http://biocyc.org/PToolsWebsiteHowto.shtml#celOverview" class="learn-more-href">Learn More</a> </p> </div> <div class="slidePic"> <picture> <source srcset="/dispatchImages/cellov2.webp" type="image/webp"> <img class="pure-img" src="/dispatchImages/cellov2.png" alt="Cellular Overview" width="582px" height="279px"> </picture> <p class="caption">Cellular Overview image generated by Pathway Tools.</p> </div> </div> <div class="slide"> <div class="slideText"> <h2 class="whitespace-none" style="font-size: 1.5em; padding-top: 10px;"><i>Helicobacter pylori</i> on your iPhone and iPad</h2> <h3 class="subhead">Have you ever wanted to quickly find out what is known about a gene, protein or pathway that was just mentioned in a talk or on a poster? Download the free BioCyc iPhone app to browse BioCyc on the go! Try the iPad version as well. </h3> <p style="line-height: 0.7em"> <a href="https://itunes.apple.com/sn/app/ecocyc/id414535548?mt=8" class="learn-more-href">Download Here</a> </p> </div> <div class="slidePic"> <picture> <source srcset="/dispatchImages/BioCyc-App-Small.webp" type="image/webp" media="(min-width: 800px)"> <source srcset="/dispatchImages/BioCyc-App-Small-w288.webp" type="image/webp"> <source srcset="/dispatchImages/BioCyc-App-Small-w288.png" media="(max-width: 799px)"> <img class="pure-img" src="/dispatchImages/BioCyc-App-Small.png" alt="BioCyc iOS App for iPhone/iPad" width="582px" height="282px"> </picture> <p class="caption">BioCyc iOS App for iPhone/iPad</p> </div> </div> <div class="slide"> <div class="slideText"> <h2 class="whitespace-none" style="font-size: 1.5em; padding-top: 10px;">RouteSearch: Search for Paths Through the Metabolic Network</h2> <h3 class="subhead">Search for lowest-cost paths through the metabolic network of the selected organism. </h3> <p style="line-height: 0.7em"> <a href="/PToolsWebsiteHowto.shtml#route_search" class="learn-more-href">Learn More</a> </p> </div> <div class="slidePic"> <picture>  <source srcset="/dispatchImages/routeSearch-w581.webp" type="image/webp">  <img class="pure-img" src="/dispatchImages/routeSearch-w581.png" alt="Route Search Diagram" width="582px" height="282px"> </picture> <p class="caption"> </p> </div> </div> <div class="slide"> <div class="slideText"> <h2 class="whitespace-none" style="font-size: 1.5em; padding-top: 10px;">Metabolic Reconstruction from Sequenced Genomes</h2> <h3 class="subhead">Install SRI's Pathway Tools software (free to academics) to predict metabolic pathways for sequenced genomes, generate metabolic models.</h3> <p style="line-height: 0.7em"> <a href="http://bioinformatics.ai.sri.com/ptools/" class="learn-more-href">Learn More</a> </p> </div> <div class="slidePic"> <img class="pure-img" src="/dispatchImages/biocyc_datacenter-cropped.jpg" width="582px" height="278px" alt="Locally Installed Omics Viewer Image"> <p class="caption"> </p> </div> </div> <div class="slide"> <div class="slideText"> <h2 class="whitespace-none" style="font-size: 1.5em; padding-top: 10px;">Gene Expression Data Analysis</h2> <h3 class="subhead">Multiple tools are available in this website for analysis of gene expression data.</h3> <p style="line-height: 0.7em"> <a href="/PToolsWebsiteHowto.shtml#omicsDataAnalysis" class="learn-more-href">Learn More</a> </p> </div> <div class="slidePic"> <picture> <source srcset="/dispatchImages/webOmics.webp" type="image/webp">  <img class="pure-img" src="/dispatchImages/webOmics.png" alt="WebOmics Image" width="581px" height="277px"> </picture> <p class="caption">Cellular Overview Omics Viewer image generated by Pathway Tools.</p> </div> </div> <div class="slide"> <div class="slideText"> <h2 class="whitespace-none" style="font-size: 1.5em; padding-top: 10px;">Comparative Genome Analysis</h2> <h3 class="subhead">Multiple comparative analysis tools are available in this website.</h3> <p style="line-height: 0.7em"> <a href="/PToolsWebsiteHowto.shtml#comparativeAnalysis" class="learn-more-href">Learn More</a> </p> </div> <div class="slidePic"> <picture>  <source srcset="/dispatchImages/multi-genome-browser.webp" type="image/webp">  <img class="pure-img" src="/dispatchImages/multi-genome-browser.png" alt="Multi-Genome Browser" width="581px" height="277px"> </picture> <p class="caption">Multi-organism Genome Browser image generated by Pathway Tools.</p> </div> </div> <div class="slide"> <div class="slideText"> <h2 class="whitespace-none" style="font-size: 1.5em; padding-top: 10px;">Search Databases by Organism Properties</h2> <h3 class="subhead">BioCyc contains data on phenotypic properties of organisms, such as human-microbiome body site, aerobicity, and temperature range. </h3> <p style="line-height: 0.7em"> <a href="/PToolsWebsiteHowto.shtml#dbselect" class="learn-more-href">Learn More</a> </p> </div> <div class="slidePic"> <img class="pure-img" src="/dispatchImages/bacteria.jpg">  <p class="caption">Image by Arek Socha from Pixabay</p> </div> </div> <div class="slide"> <div class="slideText"> <h2 class="whitespace-none" style="font-size: 1.5em; padding-top: 10px;">The BioCyc Database Collection</h2> <h3 class="subhead"> Tier 1 databases such as EcoCyc are the most highly curated. BioCyc databases are computationally derived from MetaCyc.</h3> <p style="line-height: 0.7em"> <a href="http://biocyc.org/biocyc-pgdb-list.shtml" class="learn-more-href">Learn More</a> </p> <i>   </i> <a href="/request-new-pgdb.shtml" class="learn-more-href">Request Addition of New Genome to BioCyc</a> </div> <div class="slidePic"> <picture>  <source srcset="/dispatchImages/BioCyc-tier-diagram-v1.webp" type="image/webp">  <img class="pure-img" src="/dispatchImages/BioCyc-tier-diagram-v1.png" alt="Diagram of three tiers of Databases within BioCyc" width="582px" height="279px"> </picture> <p class="caption">BioCyc Database Collection</p> </div> </div> <div class="slide"> <div class="slideText"> <h2 class="whitespace-none" style="font-size: 1.5em; padding-top: 10px;">The Omics Dashboard: A New View of Omics Data</h2> <h3 class="subhead">Visualize omics data as a set of graphs hierarchically organized by functional category. Drill down for more detail in areas of interest.</h3> <p style="line-height: 0.7em"> <a href="/dashboard/dashboard-intro.shtml" class="learn-more-href">Learn More</a> </p> </div> <div class="slidePic"> <picture>  <source srcset="/dispatchImages/dashboard.webp" type="image/webp">  <img class="pure-img" src="/dispatchImages/dashboard.png" alt="Dashboard Image" width="582px" height="278px"> </picture> <p class="caption">Cellular Dashboard image generated by Pathway Tools.</p> </div> </div> </div>   </div>  <div class="pure-u-xl-1-2 pure-u-lg-1-1 pure-u-md-1-1 pure-u-sm-1-1"> <div class="l-box-home" style="height: 510px; max-width: 590px; margin-left: auto; margin-right:auto;"> <table> <tr> <td> <h2 class="splash-head"><i>Helicobacter pylori</i> Pathway/Genome Databases</h2></td> <td><a href="https://biocyc.org"><img src="hpy.jpg" alt="Image of Helicobacter pylori organism"></a></td> </tr> </table> <p>This website contains 236 <i>Helicobacter pylori</i> genomes <a href="javascript:showChooser(false, 'Helicobacter pylori');"> (show list) </a> and associated metabolic pathways. This site is part of the larger <a href="http://biocyc.org">BioCyc</a> collection of thousands of Pathway/Genome Databases for sequenced genomes. Click the "Change Current Database" button (above) to explore the available databases. </p> <p> This site includes extensive retrieval, visualization and analysis tools, including a <a href="https://helicobacter.biocyc.org/GCF_000008525/NEW-IMAGE?type=LOCUS-POSITION&object=NIL&orgids=GCF_000008525&chromosome=CHROM-I&bp-range=1/50000">genome browser</a> and a <a href="https://helicobacter.biocyc.org/overviewsWeb/celOv.shtml?orgid=GCF_000008525">metabolic map diagram</a>. There are tools for analysis of gene expression, metabolomics and ChIP-chip data. You can search and align sequences for <i>Helicobacter pylori</i> and other microbial genomes and perform comparative analysis. You can store groups of genes and pathways into a SmartTable, and then browse, analyze and share with other users. </p> <button class="pureFreeTrial" onclick="window.location.href='/new-account.shtml'"> Try Free </button> <button class="pureFreeTrial" onclick="window.location.href='../intro.shtml'" style="width: unset"> BioCyc Intro </button> </div> </div>  </div>   <div class="pure-g" style="align-items:baseline"> <div class="pure-u-lg-1-2 pure-u-sm-1-1" style="margin-bottom: 30px;"> <h2 class="content-majorhead" style="margin-block: 0;">What people are saying </h2> </div> <div class="pure-u-lg-1-2 pure-u-sm-1-1" style="margin-bottom: 15px;"> <a href="/biocyc-testimonials.shtml"> <span style="margin-left:20px;font-size: 19px"> See more BioCyc testimonials </span></a> </div> </div> <div class="testimonialCarousel"> <div> <div class="pureOrangeQuote"><p>"BsubCyc is a tool of the utmost value."</p><img class="attribution-img" src="/graphics2021/pennState.png" alt="Penn State"></img><p class="attribution"><i>Paul Babitzke<br>Prof. of Biochemistry<br>& Molecular Biology</i></p></div> </div> <div> <div class="pureBlueQuote"><p>"My lab uses these resources on a daily basis."</p><picture><img class="attribution-img" src="/graphics2021/UWisconsin.png" style="bottom: 45px; width: 92px; height: 31px;" alt="University of Wisconsin"></img></picture><p class="attribution"><i>Patricia Kiley,<br>Professor and Chair,<br>Dep't. of Biomolecular Chemistry</i></p></div> </div> <div> <div class="pureOrangeQuote"><p style="font-size: 21px">"We rely on BioCyc's Gene Pages and Overview Diagrams almost daily."</p><img class="attribution-img" src="/graphics2021/UMinnesota.png" style="height: 46px; bottom: 20px" alt="University of Minnesota"></img><p class="attribution"><i>Arkady Khodursky<br>Assoc. Prof. Biochemistry</i></p></div> </div> <div> <div class="pureBlueQuote"><p style="font-size: 16px; padding-top: 21px">"We use BioCyc and MetaCyc extensively to investigate the metabolic and regulatory processes of organisms we study."</p> <picture><img class="attribution-img" src="/graphics2021/pnnlFlatLogo.jpg" style="bottom:23px; width: 73px; height: 31px;" alt="Pacific Northwest National Lab"></img></picture><p class="attribution" style="bottom:-12px"><i>William Cannon, Team Lead<br>Computational Biology</i></p></div> </div> <div> <div class="pureOrangeQuote"><p>"BioCyc is the go-to resource of knowledge and tools for Ginkgo scientists."</p><img class="attribution-img" src="/graphics2021/GinkgoBioworks.png" style="bottom:15px;" alt="Ginkgo Bioworks"></img><p class="attribution"><i></i></p></div> </div> <div> <div class="pureBlueQuote"><p style="font-size: 20px; padding-top: 21px">"BioCyc is a tremendous resource for pathway analysis in metabolomics."</p><img class="attribution-img" src="/graphics2021/UGA.png" style="bottom:10px" alt="University of Georgia"></img><p class="attribution" style="bottom: 15px"><i>Art Edison, Dept of Genetics</i></p></div> </div> <div> <div class="pureOrangeQuote"><p style="font-size: 18px; margin-right: 25px; padding-top: 21px">"We make extensive use of the BioCyc full metabolic network diagram for omics data analysis."</p><img class="attribution-img" src="/graphics2021/GreatLakes.png" style="bottom: 5px" alt="Great Lakes Bioenergy"></img><p class="attribution" style="bottom:15px"><i>Timothy J. Donohue, Director</i></p></div> </div> <div> <div class="pureBlueQuote"><p style="font-size: 18px; padding-top: 21px">"I have not found another database that has a better interface than BioCyc."</p><img class="attribution-img" src="/graphics2021/UMich.png" style="bottom:25px" alt="University of Michigan"></img><p class="attribution"><i>Gary B. Huffnagle, Professor<br>Microbiology and Immunology</i></p></div> </div> </div>   <div class="pure-g" style="background: #FAFAFA;"> <div class="pure-u-xl-1-1 pure-u-sm-1-1" style="padding-left: 20px"> <h2 class="content-majorhead">Learning Library</h2> </div> <div class="pure-u-xl-1-2 pure-u-lg-1-1 pure-u-sm-1-1" style="max-width:fit-content; margin-left: auto; margin-right:auto;"> <div class="l-box-home pure-hidden-phone" > <div style="width: 560px; height: 315px; margin-left: -40px"> <lite-youtube videoid="2eCrAUF0-jg" videotitle="Quick Introduction to BioCyc">  </div> </div> </div> <div class="pure-u-xl-1-2 pure-u-lg-1-1 pure-u-sm-1-1" style="max-width:fit-content; margin-left: auto; margin-right:auto;"> <div class="l-box" style="padding: 0";> <h3 style="margin-top: 3px; margin-bottom: 12px">Tutorial Videos</h3> <div class="accordion" id="AccordionWebinar"> <details> <summary>Tutorial #1: Introduction to BioCyc</summary> <div> To download or view, just click on one of the links following each segment's name. <ul> <li><a href="https://youtu.be/2eCrAUF0-jg">Quick Introduction to BioCyc (4:30) </a> <li><a href="https://youtu.be/vPbJUyyMrbo">Searching in BioCyc (17:00)</a> <li><a href="https://youtu.be/y13lfIQRd3Y">Genes (15:00)</a> <li><a href="https://www.youtube.com/watch?v=VQIYRgMXlJc">Genome Browser (11:45) </a> <li><a href="http://youtu.be/vmanLbAOlFw">Pathways (13:19) </a> <li><a href="http://youtu.be/A0POxCr7I_E">Reactions (3:37) </a> <li><a href="http://youtu.be/FjMmDLpDZb4">Compounds (6:42) </a> </ul> </div> </details> <details> <summary>Tutorial #2: Introduction to SmartTables </summary> <div> The following Tutorial will guide you through SmartTables, which enable you to create, upload, share, and analyze sets of genes, metabolites, pathways, and sequence sites. The Tutorial is broken up into parts, ranging from basic operations to more advanced uses such as gene expression analysis and metabolomics. To download or view, click one of the links below. <ul> <li><a href="https://youtu.be/lNfHYqSAkwE">SmartTables Overview (4:30)</a> <li><a href=" https://youtu.be/4nQlYQJl278">SmartTables Basics (12:43)</a> <li><a href="https://youtu.be/JsnPSgr01-c">SmartTables Transformations (8:08) </a> <li><a href=" https://youtu.be/Kc7RIDerRa8">SmartTables Import and Export (9:00) </a> <li><a href="https://youtu.be/u4KN0iFHl9o">SmartTables Gene Expression Analysis (7:40)</a> <li><a href="https://youtu.be/ZtC6-X4UrcA">Metabolomics Analysis with SmartTables (6:45) </a> </ul> </div> </details> <details> <summary>Tutorial #3: Zoomable Metabolic Map, Comparative Tools, Regulatory Network</summary> <div> This tutorial introduces users to many of the advanced tools available on the BioCyc.org website for navigating cellular networks, analyzing large-scale datasets, and comparing organisms. <ul> <li><a href="https://youtu.be/D1auFR-YtyA">The Cellular Overview: Navigating metabolic networks (17:15) </a> <li><a href="https://www.youtube.com/watch?v=edlc_pwgszw">Comparative Genomics (21:06) </a> <li><a href="https://www.youtube.com/watch?v=_25kvmBC9wE">Ortholog Viewing (10:02) </a> <li><a href="https://youtu.be/AtXsbRwBFvo">The Regulatory Overview -- exploring transcriptional regulatory networks (15:21) </a> </ul> </div> </details> <details> <summary>Tutorial #4: Omics Data Analysis</summary> <div> This tutorial will show you how to use BioCyc's tools for omics data analysis, including the cellular omics viewer, the omics dashboard, and other tools. <ul> <li><a href="https://youtu.be/k6ZUBjHDH_0">Transcriptomics Analysis Tools [brief tour (2:40) </a></li> <li> <a href="https://www.youtube.com/watch?v=gDiNdp3hnWg"> Metabolomics Analysis Tools (3:26) <a href="https://www.youtube.com/watch?v=RVkmpDTdcIU&t=2s">[click here for a detailed tutorial]</a> </li> <li><a href="https://youtu.be/lfea1lKsiWk">Omics Dashboard (16:35)</a> </li> <li> <a href="https://youtu.be/eDMcTDAMVXU">Omics Dashboard Part (24:29) </a> </li> </ul> </div> </details> <details> <summary>Tutorial #5: Pathway Collages</summary> <div> Pathway collages are multi-pathway diagrams that you can customize by, for example, overlaying omics data, altering the relative positions of pathways, and modifying connections among pathways. Learn how to generate, customize and export high-quality pathway-collage diagrams showing collections of user-specified pathways. <ul> <li> <a href="https://www.youtube.com/watch?v=WW0nVpXAusg&feature=youtu.be">Pathway Collages (22:39)</a> </li> </ul> </div> </details> <details> <summary>Tutorial #6: Creating a Pathway/Genome Database</summary> <div> Learn the entire process of building a BioCyc-like Pathway/Genome Database (PGDB) for an organism with a sequenced and annotated genome. Build a PGDB for your own lab or for the whole scientific community. <ul> <li><a href="https://youtu.be/8GTifTlmnZA">Part 1A: Introduction to Database Building and Pathologic (14:04) </a></li> <li> <a href="https://youtu.be/bn1DHXBpVQk">Part 1B: Building a Database: Detailed Pathologic Example (23:53) </a></li> <li><a href="https://youtu.be/va6UY6OdW1k">Part 2A: General Editing Strategies (8:00) </a> <li> <a href="https://youtu.be/eeMVaP9H7-k">Part 2B: Creating and Editing Reactions and Compounds (17:32)</a> <li> <a href="https://youtu.be/msYOJ3lwzck">Part 2C: Updating Proteins, Citations, GO Terms, and Enzymatic Reactions (26:10) </a> <li><a href="https://youtu.be/06kXAwJUUj0">Part 2D: Making and Editing Pathways (9:42) </a> </ul> </div> </details> <details> <summary>Tutorial #7: Using the Structured Advanced Query Page</summary> <div> An introduction to the Structured Advanced Query Page, which allows complex queries and queries across one or more databases in the BioCyc collection. You'll learn about:The basic steps of setting up an advanced query; Four examples of increasingly complex queries, including how to query across multiple databases; Where to learn more about the structure of BioCyc databases. <ul> <li><a href="https://youtu.be/3fT1T6nu3C4">Structured Advanced Query Page Quick Introduction (6:27) </a> <li> <a href="https://youtu.be/4RSexCHLbI8">Structured Advanced Query Page Full Tutorial (42:15) </a> </ul> </div> </details> </div> </div> </div> </div>      </div>  <script type="text/javascript" src="//cdn.jsdelivr.net/npm/@accessible360/accessible-slick@1.0.1/slick/slick.min.js"></script> <script type="text/javascript" src="/promoSlideShow.js"></script>  </div>   <script type="text/javascript" src="../promoSlideShow.js"></script>              <script TYPE="text/javascript" SRC="/combined/combined-1.js?v=28.5"></script>   <script type="text/javascript" src="/get-organisms-fast.js"></script> <script type="text/javascript" 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<p class="whitespace-none">  <a href="http://pathwaytools.blogspot.com">Pathway Tools Blog</a><br> <a href="/subscribe.shtml">Mailing List</a> <br><br> <a href="https://genomic.social/@biocyc" target="_blank"> <img src= "/mastodon-white.svg" alt="mastodon" rel="me" width="24" height="24"></a> <a href="https://twitter.com/BioCyc" target="_blank" onclick="this.href+='?url='+location.href"> <img src="/graphics2021/Xlogo.png" alt="twitter" width="29" height="24"></a> <a href="http://www.facebook.com/BioCyc" target="_blank"> <img src= "/graphics2021/f_logo_white.png" alt="facebook" width="24" height="24"></a> <br><br> <a href="https://biocyc.printify.me/products" target="_blank">Purchase BioCyc Mugs</a> </p> </div> </div> </div> </div> <sri-footer></sri-footer>  <div id='orgSelectorDialogCC'></div>  <div id="multiorgSelectorDialog" style="display:none" class='resizableDialog' role='dialog' aria-modal='true' aria-labeled-by='multiorgSelectorDialogTitle'> <div class="hd"><b id='multiorgSelectorDialogTitle'>Specify List of Organism Databases</b></div> <div class="bd" id="multiorgSelectorBody"> <form id="multiorgSelectorForm" action='/'> <div id='legend' style="max-width:900px"></div> <div id='multiorg3columns'> <div> <h3>Select One or More Databases: <span id="multiorgMaxLabel"></span></h3> <div id="multiorgSelectorTabs" class="orgSelectorTabs" style='min-width:504px'> <ul> <li class="selected"><a href="#multiorgNameTab">By Name</a></li> <li><a href="#multiorgTaxTab">By Taxonomy</a></li> <li><a href="#multiorgMetadataTab">By Organism Properties</a></li> <li><a href="#multiorgSavedTab">My Lists</a></li> </ul> <div id="multiorgNameTab" class='multiorgselectorTab'> <div class='orgselectorByNameContents'> <div id="multiorgRightcontent" class='nameACColumn'> <label id="multiorgFilterOptions" style="display:block;text-align:right;font-size:smaller"> Organism Filter: <select id="multiorgFilter" onChange='updateMultiOrgFilter()'> </select> </label> <div id="multiorgselectorAutoComplete"> <input id="multiorgInput" type="text" aria-label="Start typing a genus, species and/or strain name" placeholder="Start typing a genus, species and/or strain name" spellcheck=false aria-autocomplete="list" > <div id="multiorgContainer" style="font-style:italic"></div> </div> <div id="multiorgnum"></div> </div> <div class="alphabetFilter"> <div class="screen-reader-only"> <h3>Filter organisms by first letter</h3> </div> <a href="javascript:alphabetClick('a')">A</a><br> <a href="javascript:alphabetClick('b')">B</a><br> <a href="javascript:alphabetClick('c')">C</a><br> <a href="javascript:alphabetClick('d')">D</a><br> <a href="javascript:alphabetClick('e')">E</a><br> <a href="javascript:alphabetClick('f')">F</a><br> <a href="javascript:alphabetClick('g')">G</a><br> <a href="javascript:alphabetClick('h')">H</a><br> <a href="javascript:alphabetClick('i')">I</a><br> <a href="javascript:alphabetClick('j')">J</a><br> <a href="javascript:alphabetClick('k')">K</a><br> <a href="javascript:alphabetClick('l')">L</a><br> <a href="javascript:alphabetClick('m')">M</a><br> <a href="javascript:alphabetClick('n')">N</a><br> <a href="javascript:alphabetClick('o')">O</a><br> <a href="javascript:alphabetClick('p')">P</a><br> <a href="javascript:alphabetClick('q')">Q</a><br> <a href="javascript:alphabetClick('r')">R</a><br> <a href="javascript:alphabetClick('s')">S</a><br> <a href="javascript:alphabetClick('t')">T</a><br> <a href="javascript:alphabetClick('u')">U</a><br> <a href="javascript:alphabetClick('v')">V</a><br> <a href="javascript:alphabetClick('w')">W</a><br> <a href="javascript:alphabetClick('x')">X</a><br> <a href="javascript:alphabetClick('y')">Y</a><br> <a href="javascript:alphabetClick('z')">Z</a><br> </div> </div> </div> <div id="multiorgTaxTab" class='multiorgselectorTab'> <label id="multiorgTaxAutoComplete"> <span style="padding-right:5px">Search for taxon in taxonomy tree: </span> <input id="multiorgTaxName" type="text" style="width:360px" /> <div id="multiorgTaxContainer"></div> </label> <div id="multiorgTaxTreeContainer" style="min-width:489px;overflow-y:auto;margin-top:12px"> <div id="multiorgSelectorTaxTree" class="ygtv-checkbox"></div> </div> </div> <div id="multiorgMetadataTab" style="min-width:489px;overflow-y:auto" class='multiorgselectorTab' > Find organism databases according to: <ul style="line-height:118%;margin-top:4px"> <li>Organism characteristics, e.g. pathogenicity = human <li>Collection metadata, e.g. human microbiome body site = blood <li>Database properties, e.g. # (number) of Genes < 500 </ul> <div id="mclause0" class="flexRowWrap"> <select id="mmdSlot0" onChange='updateMetadataSlot(0, "m")' aria-label='Property for constraint 1'> <option value=false selected>Select Property</option> </select> <select id="mmdConstraint0" onChange='updateMetadataSlot(0, "m")' aria-label='Operator for constraint 1'> <option value="c" selected>is</option> <option value="nc">is not</option> <option value="a">has any value</option> <option value="n">has no value</option> </select> <div id="mkeywordInput0" style="display:none" class="flexRow"> <select id="mmdKeywordOp0" onchange="updateForOp(0, 'mmdKeywordOp0', 'mmdSubstringAC0', 'm')" aria-label='Operator for constraint 1'> <option value="enum" selected>Exact Match</option> <option value="substr">Substring Match</option> </select> <div class = "mdSubstringInput" id="mmdSubstringAC0"> <input id="mmdKeyword0" type="text" aria-label='Value for constraint 1'> <div id="mmdKWContainer0"></div> </div> </div> <div id="mnumericInput0" style="display:none" class="flexRow"> <select id="mmdNumOp0" onchange="updateForOp(0, 'mmdNumOp0', 'mmdNum0', 'm')" aria-label='Numeric operator for constraint 1'> <option value="e" selected>= (approx.)</option> <option value="lt"><</option> <option value="lte">≤</option> <option value="gt">></option> <option value="gte">≥</option> <option value="enum">Select Values</option> </select> <input id="mmdNum0" type="text" aria-label='Value for constraint 1'> </div> <div id="mmdEnumContainer0" style="display:none"> <select id="mmdEnum0" multiple aria-label='Value for constraint 1'> </select> </div> </div> <div id="mclause1" style="display:none"> <select id="mconnector1" aria-label='Connector for constraint 2'> <option value='AND' selected>AND</option> <option value='OR'>OR</option> </select> <input id="mmdDelete1" type="button" value ="Remove Constraint" onclick='mdRemoveClause(1, "m")' aria-label='Remove Constraint 2'> <br> <div class="flexRowWrap"> <select id="mmdSlot1" onChange='updateMetadataSlot(1, "m")' aria-label='Property for constraint 2'> <option value=false selected>Select Property</option> </select> <select id="mmdConstraint1" onChange='updateMetadataSlot(1, "m")' aria-label='Operator for constraint 2'> <option value="c" selected>is</option> <option value="nc">is not</option> <option value="a">has any value</option> <option value="n">has no value</option> </select> <div id="mkeywordInput1" style="display:none" class="flexRow"> <select id="mmdKeywordOp1" onchange="updateForOp(1, 'mmdKeywordOp1', 'mmdSubstringAC1', 'm')" aria-label='Operator for constraint 2'> <option value="enum" selected>Exact Match</option> <option value="substr">Substring Match</option> </select> <div class = "mdSubstringInput" id="mmdSubstringAC1"> <input id="mmdKeyword1" type="text" aria-label='Value for constraint 2'> <div id="mmdKWContainer1"></div> </div> </div> <div id="mnumericInput1" style="display:none" class="flexRow"> <select id="mmdNumOp1" onchange="updateForOp(1, 'mmdNumOp1', 'mmdNum1', 'm')" aria-label='Numeric operator for constraint 2'> <option value="e" selected>= (approx.)</option> <option value="lt"><</option> <option value="lte">≤</option> <option value="gt">></option> <option value="gte">≥</option> <option value="enum">Select Values</option> </select> <input id="mmdNum1" type="text" aria-label='Value for constraint 2'> </div> <div id="mmdEnumContainer1" style="display:none"> <select id="mmdEnum1" multiple aria-label='Value for constraint 2'> </select> </div> </div> </div> <div id="mclause2" style="display:none"> <select id="mconnector2" aria-label='Connector for constraint 3'> <option value='and' selected>AND</option> <option value='or'>OR</option> </select> <input id="mmdDelete2" type="button" value="Remove Constraint" onclick='mdRemoveClause(2, "m")' aria-label='Remove Constraint 3'> <br> <div class="flexRowWrap"> <select id="mmdSlot2" onChange='updateMetadataSlot(2, "m")' aria-label='Property for constraint 3'> <option value=false selected>Select Property</option> </select> <select id="mmdConstraint2" onChange='updateMetadataSlot(2, "m")' aria-label='Operator for constraint 3'> <option value="c" selected>is</option> <option value="nc">is not</option> <option value="a">has any value</option> <option value="n">has no value</option> </select> <div id="mkeywordInput2" style="display:none" class="flexRow"> <select id="mmdKeywordOp2" onchange="updateForOp(2, 'mmdKeywordOp2', 'mmdSubstringAC', 'm')" aria-label='Operator for constraint 3'> <option value="enum" selected>Exact Match</option> <option value="substr">Substring Match</option> </select> <div class = "mdSubstringInput" id="mmdSubstringAC2"> <input id="mmdKeyword2" type="text" aria-label='Value for constraint 3'> <div id="mmdKWContainer2"></div> </div> </div> <div id="mnumericInput2" style="display:none" class="flexRow"> <select id="mmdNumOp2" onchange="updateForOp(2, 'mmdNumOp2', 'mmdNum2', 'm')" aria-label='Numeric operator for constraint 3'> <option value="e" selected>= (approx.)</option> <option value="lt"><</option> <option value="lte">≤</option> <option value="gt">></option> <option value="gte">≥</option> <option value="enum">Select Values</option> </select> <input id="mmdNum2" type="text" aria-label='Value for constraint 3'> </div> <div id="mmdEnumContainer2" style="display:none"> <select id="mmdEnum2" multiple aria-label='Value for constraint 3'> </select> </div> </div> </div> <div id="mclause3" style="display:none"> <select id="mconnector3" aria-label='Connector for constraint 4'> <option value='and' selected>AND</option> <option value='or'>OR</option> </select> <input id="mmdDelete3" type="button" value="Remove Constraint" onclick='mdRemoveClause(3, "m")' aria-label='Remove Constraint 4'> <br> <div class="flexRowWrap"> <select id="mmdSlot3" onChange='updateMetadataSlot(3, "m")' aria-label='Property for constraint 4'> <option value=false selected>Select Property</option> </select> <select id="mmdConstraint3" onChange='updateMetadataSlot(3, "m")' aria-label='Operator for constraint 4'> <option value="c" selected>is</option> <option value="nc">is not</option> <option value="a">has any value</option> <option value="n">has no value</option> </select> <div id="mkeywordInput3" style="display:none" class="flexRow"> <select id="mmdKeywordOp3" onchange="updateForOp(3, 'mmdKeywordOp3', 'mmdSubstringAC3', 'm')" aria-label='Operator for constraint 4'> <option value="enum" selected>Exact Match</option> <option value="substr">Substring Match</option> </select> <div class = "mdSubstringInput" id="mmdSubstringAC3"> <input id="mmdKeyword3" type="text" aria-label='Value for constraint 4'> <div id="mmdKWContainer3"></div> </div> </div> <div id="mnumericInput3" style="display:none" class="flexRow"> <select id="mmdNumOp3" onchange="updateForOp(3, 'mmdNumOp3', 'mmdNum3', 'm')" aria-label='Numeric operator for constraint 4'> <option value="e" selected>= (approx.)</option> <option value="lt"><</option> <option value="lte">≤</option> <option value="gt">></option> <option value="gte">≥</option> <option value="enum">Select Values</option> </select> <input id="mmdNum3" type="text" aria-label='Value for constraint 4'> </div> <div id="mmdEnumContainer3" style="display:none"> <select id="mmdEnum3" multiple aria-label='Value for constraint 4'> </select> </div> </div> </div> <div id="mclause4" style="display:none"> <select id="mconnector4" aria-label='Connector for constraint 5'> <option value='and' selected>AND</option> <option value='or'>OR</option> </select> <input id="mmdDelete4" type="button" value = "Remove Constraint" onclick='mdRemoveClause(4, "m")' aria-label='Remove Constraint 5'> <br> <div class="flexRowWrap"> <select id="mmdSlot4" onChange='updateMetadataSlot(4, "m")' aria-label='Property for constraint 5'> <option value=false selected>Select Property</option> </select> <select id="mmdConstraint4" onChange='updateMetadataSlot(4, "m")' aria-label='Operator for constraint 5'> <option value="c" selected>is</option> <option value="nc">is not</option> <option value="a">has any value</option> <option value="n">has no value</option> </select> <div id="mkeywordInput4" style="display:none" class="flexRow"> <select id="mmdKeywordOp4" onchange="updateForOp(4, 'mmdKeywordOp4', 'mmdSubstringAC4', 'm')" aria-label='Operator for constraint 5'> <option value="enum" selected>Exact Match</option> <option value="substr">Substring Match</option> </select> <div class = "mdSubstringInput" id="mmdSubstringAC4"> <input id="mmdKeyword4" type="text" aria-label='Value for constraint 5'> <div id="mmdKWContainer4"></div> </div> </div> <div id="mnumericInput4" style="display:none"> <select id="mmdNumOp4" onchange="updateForOp(4, 'mmdNumOp4', 'mmdNum4', 'm')" aria-label='Numeric operator for constraint 5'> <option value="e" selected>= (approx.)</option> <option value="lt"><</option> <option value="lte">≤</option> <option value="gt">></option> <option value="gte">≥</option> <option value="enum">Select Values</option> </select> <input id="mmdNum4" type="text" aria-label='Value for constraint 5'> </div> <div id="mmdEnumContainer4" style="display:none"> <select id="mmdEnum4" multiple aria-label='Value for constraint 5'> </select> </div> </div> </div> <div id="mclause5" style="display:none"> <select id="mconnector5" aria-label='Connector for constraint 6'> <option value='and' selected>AND</option> <option value='or'>OR</option> </select> <input id="mmdDelete5" type="button" value="Remove Constraint" onclick='mdRemoveClause(5, "m")' aria-label='Remove Constraint 6'> <br> <div class="flexRowWrap"> <select id="mmdSlot5" onChange='updateMetadataSlot(5, "m")' aria-label='Property for constraint 6'> <option value=false selected>Select Property</option> </select> <select id="mmdConstraint5" onChange='updateMetadataSlot(5, "m")' aria-label='Operator for constraint 6'> <option value="c" selected>is</option> <option value="nc">is not</option> <option value="a">has any value</option> <option value="n">has no value</option> </select> <div id="mkeywordInput5" style="display:none" class="flexRow"> <select id="mmdKeywordOp5" onchange="updateForOp(5, 'mmdKeywordOp5', 'mmdSubstringAC5', 'm')" aria-label='Operator for constraint 6'> <option value="enum" selected>Exact Match</option> <option value="substr">Substring Match</option> </select> <div class = "mdSubstringInput" id="mmdSubstringAC5"> <input id="mmdKeyword5" type="text" aria-label='Value for constraint 6'> <div id="mmdKWContainer5"></div> </div> </div> <div id="mnumericInput5" style="display:none" class="flexRow"> <select id="mmdNumOp5" onchange="updateForOp(5, 'mmdNumOp5', 'mmdNum5', 'm')" aria-label='Numeric operator for constraint 6'> <option value="e" selected>= (approx.)</option> <option value="lt"><</option> <option value="lte">≤</option> <option value="gt">></option> <option value="gte">≥</option> <option value="enum">Select Values</option> </select> <input id="mmdNum5" type="text" aria-label='Value for constraint 6'> </div> <div id="mmdEnumContainer5" style="display:none"> <select id="mmdEnum5" multiple aria-label='Value for constraint 6'> </select> </div> </div> </div> <br> <div class="flexRow"> <input id="maddClause" type="button" value = "Add Constraint" onclick='mdAddClause("m")' style="display:none"> <input id="mmdSearch" type="button" value = "Find Organisms" onclick = 'processMdQuery(true, "m")'> </div> <div id="mmdResults" class='yui3-skin-sam'></div> </div> <div id="multiorgSavedTab" class='multiorgselectorTab' style="overflow-y:auto"> <div style="padding-bottom:20px"> <span>Database lists include both predefined lists and lists that are saved as SmartTables that you can edit from your <a href="/smarttables" target="new.window">My SmartTables</a> page. To add all organisms from a saved list, check the box next to the list name and then click the "Add" button. </span> </div> <div id="multiorgSavedTree" class="ygtv-checkbox"></div> <div class="requiresLogin" style="padding-top:50px"> <span class="requiresNoSavedOrglist requiresLogin"> You have no saved database lists </span> </div> <div class="requiresNotLoggedIn" style="padding-top:50px"> Log in and reload this page to access your saved database lists. </div> </div> </div> <div id="tierKey" style="padding-top:3px"> <span class="tier1">Tier 1</span> and <span class="tier2">Tier 2</span> databases are displayed with orange and blue backgrounds, respectively. </div> </div> <div class='buttons flexCol' style="gap:4px;margin:3px;"> <div id="multiorgSelectAllRow"> <input type="button" id="multiorgSelectAllBtn" class="disableWhenAllSelected" value="Select All" onclick="multiorgSelectAll()"> </div> <input type="button" id="multiorgAddToList" class="disableWhenAllSelected" value="Add →" onclick="addNewSelections()"> <input type="button" id="multiorgDeleteFromList" class="disableWhenAllSelected" value="Remove ←" onclick="deleteMultiorgOptions(false)"> <input type="button" id="multiorgClearAll" value="Clear All" onclick="deleteMultiorgOptions(true)"> <input type="button" id="moveup" value="Up ↑" onclick="moveUpOption()"> <input type="button" id="movedown" value="Down ↓" onclick="moveDownOption()"> </div> <div> <label for="multiorgSelection"><h3>Current Selection</h3></label> <span id="multiNumSelected">0</span> databases or taxa currently selected. <p> <div id='multiorgSelectionDiv'> <select multiple id="multiorgSelection"> </select> </div> <div class="requiresLogin" id="rememberAsST"> <fieldset style="border:none;padding:0"> <legend style="padding-top:3px"> Remember Selection as SmartTable:</legend> <label> <input type="radio" name="stSave" value="new" checked> Create New </label> <label> <input type="radio" name="stSave" value="old"> Update Existing </label> <div style="padding-top:3px"> <input type="text" id="orglistname" style="width:200px" placeholder="Enter SmartTable Name"> <select id="savedOrglistUpdate" class="savedOrglistSelectEl" aria-label="Select an organism SmartTable to update" style="display:none"> </select> <input type="button" value="Save" title="Clicking this button will save or update the specified organism SmartTable to refer to the currently selected databases. It will not close this dialog or submit your choices. If no databases are currently selected, clicking this button will cause the named SmartTable to be deleted. SmartTables saved here can be accessed from the My Lists tab."> </div> </fieldset> </div> <div class="requiresNotLoggedIn" style="padding-top:3px"> Note: if you create a user account and log in, you can save your database lists for next time. </div> </div> </div> </form> </div> </div> <script type="text/javascript"> multiorg_maxOrgs = 70 </script>  <script type="text/javascript"> if (forceOrgID && forceOrgID != "DEFAULT") setOrganism(forceOrgID); </script> <script src="https://unpkg.com/@popperjs/core@2"></script> <script src="https://unpkg.com/tippy.js@6"></script> <script> /* following relates to tooltips for template-top-menubar */ var subTipContent; subTipContent = "You are not connected to a paid subscription, which limits your access to BioCyc. The EcoCyc database is free."; var accelTipContent = "Create a free account and receive one month of free access to BioCyc. Even if your institution already subscribes to BioCyc, you still need to create an account for ongoing access."; if (subTipContent) { tippy('#subscribe', { content: subTipContent, theme: 'biocyc', placement: 'bottom', plugins: [hideOnEsc] }); } tippy('#account', { content: accelTipContent, theme: 'biocyc', placement: 'bottom', plugins: [hideOnEsc] }); /* following relates to tooltip for MetaCyc */ tippy('#metacycRef', { theme: 'biocyc', content: "MetaCyc is a curated database of metabolic enzymes and pathways from all domains of life.", placement: 'right', plugins: [hideOnEsc] }); </script>   <script> /* following supports Change Database button on home page (this file, index.shtml) */ var shortOrgName = "E. coli K-12 substr. MG1655"; var allOrganismsCount = "20070"; var buttonTitleString = '<i class="fa fa-window-close" onclick="changeButtonTooltip.hide()" style="float:right"></i>Searches apply to the currently selected organism database:<br><b>'+shortOrgName+'</b><br><br>Click <i>Change Current Database</i> to search one of '+ allOrganismsCount +' other organism databases.'; function qsSubmitFn () { document.getElementById('qsform').submit(); }; var changeButton = document.getElementById('changeDBBtn'); var changeButtonTooltip = tippy(changeButton, { content: buttonTitleString, theme: 'biocyc', interactive: true, allowHTML: true, placement: 'top', trigger: 'manual', offset: [0,6], }); var keyPressCount = 0; function newUserOrgCheck () { if (keyPressCount < 1) { var cookieValue = get_cookie("usedOrgChooser"); if (!cookieValue || cookieValue == "false") { changeButtonTooltip.show(); keyPressCount += 1; set_cookie("usedOrgChooser", "true"); } }}; </script> </body> </html>

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Helicobacter pylori Genome Databases