CINXE.COM
Bacterial and Viral Bioinformatics Resource Center | BV-BRC
<!DOCTYPE html> <html lang="en"> <head> <title>Bacterial and Viral Bioinformatics Resource Center | BV-BRC</title> <link rel='stylesheet' href="/js/3.42.3/p3/resources/p3.css" /> <link rel='stylesheet' href="/js/3.42.3/molstar/mol-bvbrc/molstar.css" /> <link rel='stylesheet' href="/js/3.42.3/mauve_viewer/dist/mauve-viewer.css" /> <link rel='stylesheet' href="/js/3.42.3/heatmap/dist/hotmap.css" /> <meta http-equiv="Content-Type" content="text/html; charset=utf-8"/> <meta name="Keywords" content="PATRIC, Pathosystems Resource Integration Center"/> <meta name="viewport" content="width=device-width, initial-scale=1"> <meta name="google-site-verification" content="TkjceNtwo7upCQl_gx8Zmhhp9tCmc08LitZGuvQ1Eb8" /> <link rel="manifest" href="/public/manifest.json"> <link rel="icon" sizes="16x16 32x32" href="/patric/favicon.ico"> <link href="https://fonts.googleapis.com/css2?family=Roboto+Slab:wght@300;400&family=Roboto:wght@300;400;700&display=swap" rel="stylesheet"> </head> <body class="claro patric "> <div id="ApplicationContainer" data-dojo-type="dijit/layout/BorderContainer" class="layoutContainer" data-dojo-props="id:'ApplicationContainer',gutters:false,liveSplitters:false"> <div data-dojo-type="dijit/layout/ContentPane" class="HeaderBar" data-dojo-props="region:'top'"> <div id="bv-brc-header" class="P3Header" role="heading" aria-level="1"> <div id="bv-brc-header-container"> <div class="nav-logo"> <a class="nav-logo-link" href="/"> <img class="bv-brc-logo" src="/patric/images/bv-brc/bv-brc-header-logo.png" alt="BV-BRC Logo" style="height: 28px;"/> <span><i style="color: #ffffff; font-size: 12px; padding-left: 2px;">3.42.3 </i></i></span> </a> </div> <div style="vertical-align: top; min-width: 435px; flex: 1"> <div class="topMenuButton showOnLoad dijitHidden" data-dojo-type="dijit/form/DropDownButton"> <span>ORGANISMS</span> <div data-dojo-type="p3/widget/TooltipDialog"> <div style="vertical-align: top;width:225px;display:inline-block;margin-right: 5px;"> <div class="menuHeader">Bacterial Pathogens</div> <div class="menuItems"> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/469#view_tab=overview" title="Acinetobacter overview">Acinetobacter</a> </span> <span class="menuItem half"> <a class="" title="Francisella overview" href="/view/Taxonomy/262#view_tab=overview">Francisella</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/1386#view_tab=overview" title="Bacillus overview">Bacillus</a> </span> <span class="menuItem half"> <a class="" title="Helicobacter overview" href="/view/Taxonomy/209#view_tab=overview">Helicobacter</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/773#view_tab=overview" title="Bartonella overview">Bartonella</a> </span> <span class="menuItem half"> <a class="" title="Listeria overview" href="/view/Taxonomy/1637#view_tab=overview">Listeria</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/64895#view_tab=overview" title="Borreliella overview">Borreliella</a> </span> <span class="menuItem half"> <a class="" title="Mycobacterium overview" href="/view/Taxonomy/1763#view_tab=overview">Mycobacterium</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/234#view_tab=overview" title="Brucella overview">Brucella</a> </span> <span class="menuItem half"> <a class="" title="Pseudomonas overview" href="/view/Taxonomy/286#view_tab=overview">Pseudomonas</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/32008#view_tab=overview" title="Burkholderia overview">Burkholderia</a> </span> <span class="menuItem half"> <a class="" title="Rickettsia overview" href="/view/Taxonomy/780#view_tab=overview">Rickettsia</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/194#view_tab=overview" title="Campylobacter overview">Campylobacter</a> </span> <span class="menuItem half"> <a class="" title="Salmonella overview" href="/view/Taxonomy/590#view_tab=overview">Salmonella</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/810#view_tab=overview" title="Chlamydia overview">Chlamydia</a> </span> <span class="menuItem half"> <a class="" title="Shigella overview" href="/view/Taxonomy/620#view_tab=overview">Shigella</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/1485#view_tab=overview" title="Clostridium overview">Clostridium</a> </span> <span class="menuItem half"> <a class="" title="Staphylococcus overview" href="/view/Taxonomy/1279#view_tab=overview">Staphylococcus</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/776#view_tab=overview" title="Coxiella overview">Coxiella</a> </span> <span class="menuItem half"> <a class="" title="Streptococcus overview" href="/view/Taxonomy/1301#view_tab=overview">Streptococcus</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/943#view_tab=overview" title="Ehrlichia overview">Ehrlichia</a> </span> <span class="menuItem half"> <a class="" title="Vibrio overview" href="/view/Taxonomy/662#view_tab=overview">Vibrio</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/561#view_tab=overview" title="Escherichia overview">Escherichia</a> </span> <span class="menuItem half"> <a class="" title="Yersinia overview" href="/view/Taxonomy/629#view_tab=overview">Yersinia</a> </span> </div> <br> <div> <span class="menuItem half"> <a class="" href="/view/Bacteria/2" title="Overview page for all Bacteria genomes">All Bacteria</a> </span> <span class="menuItem half"> <a class="" href="/view/Taxonomy/2157" title="Overview page for all Archea genomes">All Archaea</a> </span> <span class="menuItem half"> <a class="" href="/view/Taxonomy/10239" title="Overview page for all Viruses">All Viruses</a> </span> <span class="menuItem half"> <a class="" href="/view/Host/?eq(taxon_lineage_ids,2759)#view_tab=genomes" title="Overview page for all Eukaryotic host genomes">Eukaryotic Hosts</a></span> </div> </div> </div> <div style="vertical-align: top;width:341px;display:inline-block;margin-right: 5px;"> <div class="menuHeader">Viral Families</div> <div class="menuItems"> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/10508#view_tab=overview" title="Adenoviridae overview">Adenoviridae</a> </span> <span class="menuItem half"> <a class="" title="Orthomyxoviridae overview" href="/view/Taxonomy/11308#view_tab=overview">Orthomyxoviridae</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/137992#view_tab=overview" title="Asfarviridae overview">Asfarviridae</a> </span> <span class="menuItem half"> <a class="" title="Paramyxoviridae overview" href="/view/Taxonomy/11158#view_tab=overview">Paramyxoviridae</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/1980410#view_tab=overview" title="Bunyavirales overview">Bunyavirales</a> </span> <span class="menuItem half"> <a class="" title="Parvoviridae overview" href="/view/Taxonomy/10780#view_tab=overview">Parvoviridae</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/11974#view_tab=overview" title="Caliciviridae overview">Caliciviridae</a> </span> <span class="menuItem half"> <a class="" title="Picornaviridae overview" href="/view/Taxonomy/12058#view_tab=overview">Picornaviridae</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/11118#view_tab=overview" title="Coronaviridae overview">Coronaviridae</a> </span> <span class="menuItem half"> <a class="" title="Pneumoviridae overview" href="/view/Taxonomy/11244#view_tab=overview">Pneumoviridae</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/11266#view_tab=overview" title="Filoviridae overview">Filoviridae</a> </span> <span class="menuItem half"> <a class="" title="Polyomaviridae overview" href="/view/Taxonomy/151341#view_tab=overview">Polyomaviridae</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/11050#view_tab=overview" title="Flaviviridae overview">Flaviviridae</a> </span> <span class="menuItem half"> <a class="" title="Poxviridae overview" href="/view/Taxonomy/10240#view_tab=overview">Poxviridae</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/10404#view_tab=overview" title="Hepadnaviridae overview">Hepadnaviridae</a> </span> <span class="menuItem half"> <a class="" title="Reovirales overview" href="/view/Taxonomy/2732541#view_tab=overview">Reovirales</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/291484#view_tab=overview" title="Hepeviridae overview">Hepeviridae</a> </span> <span class="menuItem half"> <a class="" title="Rhabdoviridae overview" href="/view/Taxonomy/11270#view_tab=overview">Rhabdoviridae</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/548681#view_tab=overview" title="Herpesvirales overview">Herpesvirales</a> </span> <span class="menuItem half"> <a class="" title="Togaviridae overview" href="/view/Taxonomy/11018#view_tab=overview">Togaviridae</a> </span> </div> </div> <div class="menuHeader">Featured Viruses</div> <div class="menuItems"> <div> <span class="menuItem half"> <a class="" href="/view/GenomeList/?eq(genome_name,phage)" title="Bacteriophages overview">Bacteriophages</a> </span> <span class="menuItem half"> <a class="" title="Influenza A virus overview" href="/view/Taxonomy/11320#view_tab=overview">Influenza A virus</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/12637#view_tab=overview" title="Dengue virus overview">Dengue virus</a> </span> <span class="menuItem half"> <a class="" title="Mammarenavirus lassaense overview" href="/view/Taxonomy/3052310#view_tab=overview">Mammarenavirus lassaense</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/186536#view_tab=overview" title="Ebolavirus overview">Ebolavirus</a> </span> <span class="menuItem half"> <a class="" title="Monkeypox virus overview" href="/view/Taxonomy/10244#view_tab=overview">Monkeypox virus</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/12059#view_tab=overview" title="Enterovirus overview">Enterovirus</a> </span> <span class="menuItem half"> <a class="" title="SARS-CoV-2 overview" href="/view/Taxonomy/2697049#view_tab=overview">SARS-CoV-2</a> </span> </div> <div> <span class="menuItem half"> <a class="" href="/view/Taxonomy/11102#view_tab=overview" title="Hepacivirus overview">Hepacivirus</a> </span> <span class="menuItem half"> <a class="" title="Zika virus overview" href="/view/Taxonomy/64320#view_tab=overview">Zika virus</a> </span> </div> </div> </div> </div> </div> <div class="topMenuButton showOnLoad dijitHidden" data-dojo-type="dijit/form/DropDownButton"> <span>SEARCHES</span> <div data-dojo-type="p3/widget/TooltipDialog"> <div class="menuHeader" style="padding-right: 20px;">Advanced Search</div> <div><a class="navigationLink" href="/searches/TaxaSearch">Taxa</a></div> <div><a class="navigationLink" href="/searches/GenomeSearch">Genomes</a></div> <div><a class="navigationLink" href="/searches/StrainSearch">Strains</a></div> <div><a class="navigationLink" href="/searches/GenomicFeatureSearch">Features</a></div> <div><a class="navigationLink" href="/searches/ProteinSearch">Proteins</a></div> <div><a class="navigationLink" href="/searches/SpecialtyGeneSearch">Specialty Genes</a></div> <div><a class="navigationLink" href="/searches/DomainAndMotifSearch">Domains and Motifs</a></div> <div><a class="navigationLink" href="/searches/EpitopeSearch">Epitopes</a></div> <div><a class="navigationLink" href="/searches/ProteinStructureSearch">Protein Structures</a></div> <div><a class="navigationLink" href="/searches/PathwaySearch">Pathways</a></div> <div><a class="navigationLink" href="/searches/SubsystemSearch">Subsystems</a></div> <div><a class="navigationLink" href="/searches/SurveillanceSearch">Surveillance</a></div> <div><a class="navigationLink" href="/searches/SerologySearch">Serology</a></div> <div><a class="navigationLink" href="/searches/SFVTSearch">Sequence Feature Variant Types</a></div> </div> </div> <div class="topMenuButton showOnLoad dijitHidden" data-dojo-type="dijit/form/DropDownButton"> <span>TOOLS & SERVICES</span> <div data-dojo-type="p3/widget/TooltipDialog"> <div> <div style="vertical-align: top;width:250px;margin-right:5px;display:inline-block"> <div class="menuHeader">Genomics</div> <div class="menuItems"> <a class="navigationLink" href="/app/Assembly2">Genome Assembly</span></a> <div><a class="navigationLink" href="/app/Annotation">Genome Annotation</a></div> <div><a class="navigationLink" href="/app/ComprehensiveGenomeAnalysis">Comprehensive Genome Analysis <span style="font-style: italic;">(B)</span></a></div> <div><a class="navigationLink" href="/app/Homology">BLAST</a></div> <div><a class="navigationLink" href="/app/PrimerDesign">Primer Design</a></div> <div><a class="navigationLink" href="/app/GenomeDistance">Similar Genome Finder</div> <div><a class="navigationLink" href="/app/GenomeAlignment">Genome Alignment</span></a></div> <div><a class="navigationLink" href="/app/Variation">Variation Analysis</a></div> <div><a class="navigationLink" href="/app/Tnseq">Tn-Seq Analysis</a></div> </div> <div class="menuHeader">Phylogenomics</div> <div class="menuItems"> <div><a class="navigationLink" href="/app/PhylogeneticTree">Bacterial Genome Tree</a></div> <div><a class="navigationLink" href="/app/ViralGenomeTree">Viral Genome Tree</a></div> <div><a class="navigationLink" href="/app/GeneTree">Gene/Protein Tree</a></div> </div> <div class="menuHeader">Protein Tools</div> <div class="menuItems"> <div><a class="navigationLink" href="/app/MSA">MSA and SNP Analysis</a></div> <div><a class="navigationLink" href="/app/MetaCATS">Meta-CATS</a></div> <div><a class="navigationLink" href="/app/SeqComparison">Proteome Comparison</a></div> <div><a class="navigationLink" href="/app/ComparativeSystems">Protein Family Sorter</a></div> <div><a class="navigationLink" href="/app/ComparativeSystems">Comparative Systems</a></div> <div><a class="navigationLink" href="/app/Docking">Docking</a></div> </div> </div> <div style="vertical-align:top;width:250px;display:inline-block"> <div class="menuHeader">Metagenomics</div> <div class="menuItems"> <div><a class="navigationLink" href="/app/TaxonomicClassification">Taxonomic Classification</a></div> <div><a class="navigationLink" href="/app/MetagenomicBinning">Metagenomic Binning</a></div> <div><a class="navigationLink" href="/app/MetagenomicReadMapping">Metagenomic Read Mapping</a></div> </div> <div class="menuHeader">Transcriptomics</div> <div class="menuItems"> <div><a class="navigationLink" href="/app/Rnaseq">RNA-Seq Analysis</a></div> <div><a class="navigationLink" href="/app/Expression">Expression Import</a></div> </div> <p></p> <div class="menuHeader">Utilities</div> <div class="menuItems"> <div><a class="navigationLink" href="/app/FastqUtil">Fastq Utilities</a></div> <div><a class="navigationLink" href="/app/IDMapper">ID Mapper</a></div> </div> <p></p> <div class="menuHeader">Viral Tools</div> <div class="menuItems"> <div><a class="navigationLink" href="/app/ComprehensiveSARS2Analysis">SARS-CoV-2 Genome Analysis</a></div> <div><a class="navigationLink" href="/app/SARS2Wastewater">SARS-CoV-2 Wastewater Analysis</a></div> <div><a class="navigationLink" href="/app/SequenceSubmission">Influenza Sequence Submission</a></div> <div><a class="navigationLink" href="/app/HASubtypeNumberingConversion">Influenza HA Subtype Conversion</a></div> <div><a class="navigationLink" href="/app/SubspeciesClassification">Subspecies Classification</a></div> </div> <p></p> <div class="menuHeader">Outbreak Tracker</div> <div class="menuItems"> <div><b><a class="navigationLink" href="/outbreaks/Mpox/#view_tab=overview">Mpox 2024</a></b></div> <div><b><a class="navigationLink" href="/outbreaks/H5N1/#view_tab=overview">Influenza H5N1 2024</a></b></div> <div><b><a class="navigationLink" href="/outbreaks/SARSCoV2/#view_tab=overview">SARS-CoV-2</a></b></div> </div> </div> </div> </div> </div> <div class="topMenuButton showOnLoad dijitHidden" data-dojo-type="dijit/form/DropDownButton"> <span>WORKSPACES</span> <div data-dojo-type="p3/widget/TooltipDialog"> <div> <div style="vertical-align: top;width:175px;display:inline-block"> <div class="HideWithAuth"> Please <a class="loginLink">sign in</a> to view your workspaces. </div> <div class="ShowWithAuth"> <div><i class="fa icon-caret-down fa-1x noHoverIcon" style="color:#333;cursor:normal;"></i> <a class="navigationLink" id="YourWorkspaceLink">Workspaces</a></div> <div id="YourWorkspaces"></div> <div><a class="navigationLink" href="/workspace/public">Public Workspaces</a></div> <div><a class="navigationLink" href="/workspace/public/ARWattam@patricbrc.org/BV-BRC%20Workshop">BV-BRC Workshop</a></div> </div> </div> <div style="vertical-align:top;display:inline-block" class="ShowWithAuth"> <div> <a class="navigationLink" href="/job/">My Jobs</a> </div> <div> <a class="navigationLink" href="/view/GenomeList/?eq(public,false)">My Genomes</a> </div> </div> </div> </div> </div> <div class="topMenuButton showOnLoad dijitHidden" data-dojo-type="dijit/form/DropDownButton"> <span>HELP</span> <div data-dojo-type="p3/widget/TooltipDialog"> <div style="font-weight: bold; font-size: 14px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/">Documentation Website</a></div> <div style="margin-top: 5px; margin-bottom: 5px;" class="menuHeader">Updates and Reports</div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/news/index.html">News and Announcements</a></div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/reports_and_analysis/index.html">Reports and Analysis</a></div> <div style="margin-top: 5px; margin-bottom: 5px;" class="menuHeader">Help Resources</div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/overview.html">Overview</a></div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/quick_start/index.html">Quick Start</a></div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/data_protocols/index.html">Data Sources & Protocols</a></div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/quick_references/index.html">Quick Reference Guides</a></div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/tutorial/index.html">Tutorials</a></div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/common_tasks/index.html">Common Tasks</a></div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/cli_tutorial/index.html">Command Line Interface</a></div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/videos/index.html">Instructional Videos</a></div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/webinar/index.html">Webinars</a></div> <div style="margin-bottom: 5px;" class="menuHeader">System Documentation</div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/system_documentation/system_architecture.html">System Architecture</a></div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/test_procedures/index.html">Test Procedures</a></div> <div style="margin-left: 10px;"><a class="navigationLinkOut" href="https://www.bv-brc.org/docs/usage_metrics.html">Usage Metrics</a></div> </div> </div> <div class="topMenuButton showOnLoad dijitHidden" data-dojo-type="dijit/form/DropDownButton"> <span>ABOUT</span> <div data-dojo-type="p3/widget/TooltipDialog"> <div><a class="TopMenuLink" href="/about">About BV-BRC</a></div> <div><a class="DialogButton" rel="reportProblem:">Contact Us</a></div> <div><a class="TopMenuLink" href="/team">Our Team</a></div> <div><a class="TopMenuLink" href="https://www.bv-brc.org/docs/news/index.html" target="_blank">Announcements</a></div> <div><a class="TopMenuLink" href="/brc-calendar">BRC Calendar</a></div> <hr> <div><a class="TopMenuLink" href="/publications">Publications</a></div> <div><a class="TopMenuLink" href="/citation">Citation</a></div> <div><a class="TopMenuLink" href="/related-resources">Related Resources</a></div> <div><a class="TopMenuLink navigationLinkOut" href="https://github.com/BV-BRC" target="_blank" rel="noopener">BV-BRC GitHub</a></div> <div><a class="TopMenuLink" href="/privacy-policy">Privacy Policy</a></div> </div> </div> </div> <div id="p3header-search" style="padding: 6px 10px 2px 2px; width: 120px; flex-grow: 0.85"> <input style="width:100%;font-size:1em;" class="showOnLoad dijitHidden" data-dojo-type="p3/widget/GlobalSearch"/> </div> <!-- <div class="navbar-flex-space" style="flex-grow: 0.85;"></div> --> <div class="HideWithAuth authLinks showOnLoad dijitHidden" style="padding: 8px 10px 0 0;"> <a class="LoginButton navigationLink" href="/register">Register</a> <a class="LoginButton navigationLink" href="/login">Sign In</a> </div> <div class="showOnLoad ShowWithAuth dijitHidden"> <div class="showOnLoad ShowWithAuth dijitHidden topMenuButtonIcon" data-dojo-type="dijit/form/DropDownButton" data-dojo-props="iconClass:'icon-user fa-2x login-btn'"> <span></span> <div class="warning_icon user_warning_icon icon-warning fa fa-1x"> </div> <div data-dojo-type="p3/widget/TooltipDialog"> <div>Signed in as <span id="signedInAs" style="font-weight:bold;"></span></div> <hr> <div><a class="userProfile">Account Settings <i class="warning_icon account-settings-warning icon-warning fa fa-1x" style="vertical-align:middle;"> </i></a></div> <div><a class="sulogin">SU Login</a></div> <div><a class="suSwitchBack" onclick="window.App.suSwitchBack()" style="display:none">SU Switch Back</a></div> <div><a class="logoutLink" onclick="window.App.logout()">Logout</a></div> </div> </div> </div> </div> </div> <!-- --> <!-- <div class="msg-box-below-topnav"><strong>The BV-BRC scheduler will be undergoing maintenance on June 6, from 9:00AM-Noon (Chicago Time). Already running jobs will not be affected but job status and submission of new jobs will be unavailable. We are sorry for the inconvenience. -- BV-BRC Team</strong></div> --> <!-- <div class="msg-box-below-topnav"><strong>Welcome to the BV-BRC Alpha website. This site is used for active development and testing of the BV-BRC resource. Hence, the data and functionality may change frequently and without notice.</strong></div> --> <!-- <div class="msg-box-below-topnav"><strong>Welcome to the BV-BRC Beta website. This site is used to seek early community feedback for the BV-BRC resource, which is still under development. Please note that the data and functionality on this site may change frequently and without notice.</strong></div> --> </div> <div data-dojo-type="dijit/layout/ContentPane" data-dojo-props="region:'center'" style="padding:0px;border:0px solid #ddd;background:inherit;"> <div id="bv-brc-home"> <div class="verification_message home-banner"> <p> <strong>Your email has not been verified. Click here to visit your profile and update your email address and/or resend the verification message.</strong> </p> </div> <!--<div class="top-banner-flex"> <div class="top-banner"> <!-- <p> We are pleased to welcome our PATRIC users to the release of the new Bacterial and Viral Bioinformatics Resource Center (BV-BRC). BV-BRC combines the data, tools, and technologies from the bacterial BRC (<a href="https://legacy.patricbrc.org" class="navigationLinkOut">Legacy PATRIC</a>) and the viral BRCs (<a href="https://www.fludb.org/brc/home.spg?decorator=influenza" class="navigationLinkOut">IRD</a> and <a href="https://www.viprbrc.org/brc/home.spg?decorator=vipr" class="navigationLinkOut">ViPR</a>) and will be replacing them entirely in the near future. You can learn more about the transition <a href="https://www.bv-brc.org/docs/news/2022/20220816-bv-brc-patric-redirect.html" class="navigationLinkOut">here</a>. </p> <!-- <p> Dear <a href="https://legacy.fludb.org" class="navigationLinkOut" style="font-weight: bold;">IRD</a> and <a href="https://legacy.viprbrc.org" class="navigationLinkOut" style="font-weight: bold;">ViPR</a> users, welcome to <a href="https://www.bv-brc.org/docs/overview.html" class="navigationLinkOut" style="font-weight: bold;">BV-BRC</a>. The migration of the data, tools, and services from the legacy IRD and ViPR applications to BV-BRC is now <strong>complete</strong>. All web traffic from the <strong>IRD</strong> and <strong>ViPR</strong> resources is also being forwarded to the BV-BRC home page. Please refer to this <a href="https://www.bv-brc.org/docs/quick_start/index.html" class="navigationLinkOut" style="font-weight: bold;">Quick Start Guide</a> to learn how to start using <strong>BV-BRC</strong>. <br> <br> If you have questions or need assistance, please contact us at <a href="mailto:help@bv-brc.org" style="font-weight: bold;">help@bv-brc.org</a>. </p> </div> </div> --> <div id="bv-brc-home-container"> <div class="grid-container"> <div class="bv-brc-info"> <h1>BACTERIAL AND VIRAL BIOINFORMATICS RESOURCE CENTER</h1> <p> Welcome to the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), an information system designed to support research on bacterial and viral infectious diseases. The BV-BRC combines the data and tools from the Legacy BRC resources: PATRIC, the bacterial BRC, and IRD and ViPR, the viral BRCs. If you are transitioning from PATRIC or IRD/ViPR, please refer to the <a href="https://www.bv-brc.org/docs/quick_start/index.html" class="navigationLinkOut" style="font-weight: bold;">Quick Start Guide</a> to learn how to get started with BV-BRC. Please <a href="mailto:help@bv-brc.org" style="font-weight: bold;">contact us</a> if you have any questions or issues. </p> <div class="search" style="display: flex; align-items: center; justify-content: space-between;"> <h3>SEARCH</h3> <div class="global-search" style="flex-grow: 5;"> <div style="padding: 6px 0px 2px 2px; flex-grow: 1"> <input style="width:100%;font-size:1em;" class="showOnLoad dijitHidden" data-dojo-type="p3/widget/GlobalSearch" /> </div> </div> </div> <div class="browse" style="display: flex; align-items: center; justify-content: space-between;"> <h3>BROWSE</h3> <a href="/view/Bacteria/2" class="btn btn-blue" style="width: 125px;">BACTERIA</a> <a href="/view/Taxonomy/2157" class="btn btn-blue" style="width: 125px;">ARCHAEA</a> <a href="/view/Virus/10239" class="btn btn-blue" style="width: 125px;">VIRUSES</a> <a href="/view/Host/?eq(taxon_lineage_ids,2759)#view_tab=genomes" class="btn btn-blue" style="width: 150px;">EUKARYOTIC HOSTS</a> </div> </div> <div class="bv-brc-mid"><!-- style="grid-row: 3/6"--> <div class="bv-brc-mid-content"> <h2>ANALYZE DATA IN BV-BRC</h2> <p style="padding-bottom: 20px;">Upload and analyze your data in the private workspace. <span class="HideWithAuth"><a href="/register" style="font-weight: bold;">Register</a> or <a href="/login" style="font-weight: bold;">Login</a> to get started.</p></span> <div class="bv-brc-mid-content-links"> <div class="mid-links"> <h3>SEARCH</h3> <a href="/searches/TaxaSearch" class="navigationLink">Taxa</a> <a href="/searches/GenomeSearch" class="navigationLink">Genomes</a> <a href="/searches/ProteinSearch" class="navigationLink">Proteins</a> <a href="/searches/SpecialtyGeneSearch" class="navigationLink">Specialty Genes</a> <a href="/searches" style="text-decoration: underline;">All Searches...</a> </div> <div class="mid-links"> <h3>ANALYZE</h3> <a href="/app/Assembly2" class="navigationLink">Assembly</a> <a href="/app/Annotation" class="navigationLink">Annotation</a> <a href="/app/Homology" class="navigationLink">BLAST</a> <a href="/app/MSA" class="navigationLink">MSA</a> <a href="/tools" style="text-decoration: underline;">All Tools & Services...</a> </div> <div class="mid-links"> <h3>MANAGE DATA</h3> <a href="https://bv-brc.org/docs/quick_references/workspaces/workspace.html" class="navigationLinkOut">Access Private Workspace</a> <a href="https://bv-brc.org/docs/quick_references/workspaces/groups.html" class="navigationLinkOut">Save Search Results</a> <a href="https://bv-brc.org/docs/quick_references/workspaces/data_upload.html" class="navigationLinkOut">Upload Data</a> <a href="https://bv-brc.org/docs/quick_references/workspaces/jobs.html" class="navigationLinkOut">Access Analysis Jobs</a> <a href="https://bv-brc.org/docs/quick_references/workspaces/workspace.html#creating-and-sharing-workspaces" class="navigationLinkOut">Share and Publish</a> </div> <div class="mid-links"> <h3>BATCH ACCESS</h3> <a href="https://bv-brc.org/docs/cli_tutorial/index.html" class="navigationLinkOut">Command-Line Interface</a> <a href="https://bv-brc.org/api/doc/" class="navigationLinkOut">Data API</a> <a href="https://bv-brc.org/docs/quick_references/ftp.html" class="navigationLinkOut">FTP</a> </div> </div> </div> <div class="mid-content-bottom"> <div class="mid-content-buttons"> <a href="https://bv-brc.org/docs/quick_start/index.html" class="btn btn-blue navigationLinkOut" style="width: 125px">QUICK START</a> <a href="https://bv-brc.org/docs/quick_references/index.html" class="btn btn-blue navigationLinkOut" style="width: 150px;">REFERENCE GUIDES</a> <a href="https://bv-brc.org/docs/tutorial/index.html" class="btn btn-blue navigationLinkOut" style="width: 125px;">TUTORIALS</a> </div> </div> </div> <div class="bv-brc-bottom-left" style="max-height: 250px;"> <div class="bottom-left-content"> <h2>Information for PATRIC Users</h2> <img src="/patric/images/bv-brc/patric-logo.png" alt="PATRIC Logo"> <p> The new BV-BRC system is built on the PATRIC system. Viral data and analysis tools and services from IRD/ViPR have now been integrated into the resource. </p> <br> <div class="bottom-left-content-links"> <a href="https://www.bv-brc.org/docs/quick_start/data_functionality_overview.html" class="navigationLinkOut">BV-BRC Data and Functionality Overview</a> </div> </div> </div> <div class="bv-brc-bottom-right" style="max-height: 250px;"> <div class="bottom-right-content"> <h2>Information for IRD/ViPR Users</h2> <img class="ird-vipr-logo" src="/patric/images/bv-brc/ird-vipr-logo.png" alt="IRD and ViPR Logo"> <p> The new BV-BRC system is built on the PATRIC Bacterial BRC system and incorporates data and tools from IRD and ViPR. The following materials are designed to aid IRD and ViPR users in using BV-BRC. </p> <br> <div class="bottom-right-content-links"> <a href="https://www.bv-brc.org/docs/quick_start/ird-vipr_bv-brc_mapping.html" class="navigationLinkOut">IRD/ViPR to BV-BRC Mapping </a> <!-- <a href="https://www.bv-brc.org/docs/quick_start/common_tasks.html" class="navigationLinkOut">Common Tasks in BV-BRC</a> --> </div> </div> </div> <div class="outbreaks bv-brc-mid-content-links"> <h2>OUTBREAKS</h2> <div class="mid-links"> <a href="/outbreaks/Mpox/#view_tab=overview" style="line-height: 1.1em"><b>Mpox 2024</b></a> <a href="/outbreaks/H5N1/#view_tab=overview" style="line-height: 1.1em"><b>Influenza H5N1 2024</b></a> <a href="/outbreaks/SARSCoV2/#view_tab=overview" style="line-height: 1.1em"><b>SARS-CoV-2</b></a> </div> </div> <div class="announcements"> <h2>NEWS & ANNOUNCEMENTS</h2> <ul class="slides" id="announcements-slides"></ul> <div class="dot-navigation" id="announcements-dot-navigation" style="margin-top: 285px;"></div> </div> <div class="linkedin-feed" id="linkedin-feed"> <h2 style="margin-bottom: 0;">COMMUNITY NEWS</h2> <ul class="slides" id="linkedin-slides" style="height: 84%;"></ul> <div class="dot-navigation" id="linkedin-dot-navigation" style="margin-top: 15px;"></div> </div> </div> </div> </div> <footer id="bv-brc-footer"> <div id="bv-brc-footer-container"> <div class="col col-1"> <h3>BRC Program</h3> <a href="https://www.niaid.nih.gov/research/bioinformatics-resource-centers"><img src="/patric/images/bv-brc/brc-logo.png" alt="BRC Logo" style="margin-left: -50px;"></a> <!-- <ul> <li><a class="navigationLinkOut" href="https://www.niaid.nih.gov/research/bioinformatics-resource-centers">NIAID</a></li> <li><a href="https://www.patricbrc.org">PATRIC</a></li> <li><a class="navigationLinkOut" href="https://www.viprbrc.org/brc/home.spg?decorator=vipr">ViPR</a></li> <li><a class="navigationLinkOut" href="https://www.fludb.org/brc/home.spg?decorator=influenza">IRD</a></li> <li><a class="navigationLinkOut" href="https://eupathdb.org/eupathdb/">EuPathDB</a></li> <li><a class="navigationLinkOut" href="https://www.vectorbase.org/">VectorBase</a></li> </ul> --> </div> <div class="col col-2"> <h3>Funding Statement</h3> <p>This project has been funded in whole or in part with Federal funds from the National Institute of Allergy and Infectious Diseases, National Institutes of Health, Department of Health and Human Services, under Grant No. U24AI183849, awarded to the University of Chicago.</p> </div> <div class="col col-3"> <h3>Follow Us</h3> <a href="https://twitter.com/BVBRC_DB" target="=_blank"><span class="icon-twitter-square fa-3x"></span></a> <a href="https://www.facebook.com/BVBRC19" target="=_blank"><span class="icon-facebook-square fa-3x"></span></a> <a href="https://www.youtube.com/c/BVBRC" target="=_blank"><span class="icon-youtube-square fa-3x"></span></a> <a href="https://reddit.com/r/BRC_users" target="=_blank"><span class="icon-reddit-square fa-3x"></span></a> <a href="https://github.com/BV-BRC" target="=_blank"><span class="icon-github-square fa-3x"></span></a> </div> </div> </footer> <style> body.patric { min-width: 830px; } #p3header-search { display: none; } </style> </div> </div> <script> dojoConfig = { parseOnLoad: false, packages: [ {name: 'lazyload', location: "../lazyload", main: 'lazyload'}, {name: 'jDataView', location: '../jDataView/src', main: 'jdataview'}, {name: "FileSaver", location: "../FileSaver", main: "FileSaver"} ] } </script> <!-- Scripts --> <script type="text/javascript" src="/js/3.42.3/mauve_viewer/dist/mauve-viewer.js"></script> <script type="text/javascript" src="/js/3.42.3/msa/dist/msa.min.js"></script> <script type="text/javascript" src="/js/3.42.3/bvbrc_js_client/dist/bvbrc_client.js"></script> <script type="text/javascript" src="/js/3.42.3/bundle/bundle.js"></script> <script type="text/javascript" src="/js/3.42.3/bundle/bundle2.js"></script> <script type="text/javascript"> $(window).on('load', function () { // LinkedIn Feed let $linkedInFeedElm = $("#linkedin-feed"); // Fetch the data only if feed element exists in the page if ($linkedInFeedElm.length) { $.getJSON({ url: '/linkedin/posts/?count=8', success: function (data) { for (let post of data.elements) { if (post.id && post.id.includes('share')) { $("#linkedin-slides").append( `<li class="slide" style="height: 100%;"> <div class="iframe-container" style="position: relative; width: 100%; height: 100%;"> <div class="iframe-placeholder" style="position: absolute; top: 50%; left: 50%; transform: translate(-50%, -50%); z-index: 1; transition: opacity 0.3s ease;"> <p>Loading the news...</p> </div> <iframe data-src="https://www.linkedin.com/embed/feed/update/${post.id}" style="height: 100%; width: 100%; opacity: 0; border: none; transition: opacity 0.3s ease;" loading="lazy"></iframe> </div> </li>` ); $("#linkedin-dot-navigation").append( `<div class="dot" role="button" aria-selected="false"></div>` ); } } initializeSlide($('#linkedin-slides .slide'), $("#linkedin-dot-navigation .dot")); }, error: function (data) { console.log(data); } }); } // News & Announcements Carousel $.getJSON("https://www.bv-brc.org/docs/_static/carousel.json", function (feed) { for (var i = 0; i < feed.length; i++) { var link = feed[i].link; var title = feed[i].title; var desc = feed[i].desc; var word_limit = (feed[i].img == "") ? 60 : 20 var descSnippit = desc.split(" ", word_limit).join(" "); var img = feed[i].img; $("#announcements-slides").append( `<li class="slide"> <a href="${link}" class="feed-link"> <h4 class="feed-title">${title}</h4> </a> <p class="feed-description">${descSnippit} ... <a href="${link}">read more</a></p> <img src="${img}" class="feed-img" loading="lazy"> </li>` ); $("#announcements-dot-navigation").append( `<div class="dot" role="button" aria-selected="false"></div>` ); } initializeSlide($('#announcements-slides .slide'), $("#announcements-dot-navigation .dot")); }); }); function initializeSlide($slides, $dots) { $slides.first().addClass("showing current-slide"); $dots.first().addClass("selected current-dot").attr('aria-selected', 'true'); let index = 0; loadSlide($slides.eq(index)); $dots.click(function () { $dots.eq(index).removeClass("current-dot").attr('aria-selected', 'false'); $slides.eq(index).removeClass("current-slide"); $(this).addClass("current-dot").attr('aria-selected', 'true'); index = $(this).index(); $slides.eq(index).addClass("current-slide"); loadSlide($slides.eq(index)); }); } function loadSlide(slide) { const $iframeContainer = slide.find('.iframe-container'); const $iframe = $iframeContainer.find('iframe'); const $placeholder = $iframeContainer.find('.iframe-placeholder'); // Only load the iframe if it's not already loaded if ($iframe.length && !$iframe.attr('src')) { const dataSrc = $iframe.attr('data-src'); // Bind the load event before setting the src $iframe.on('load', function () { $placeholder.fadeOut(300, function () { $iframe.css('opacity', 1); }); }); $iframe.attr('src', dataSrc); $iframe.css('opacity', 0); // Start hidden } } </script> <!-- // use bundle.js <script type="text/javascript" src="/js/cytoscape/dist/cytoscape.min.js"></script> <script type="text/javascript" src="/js/jquery/dist/jquery.min.js"></script> <script type="text/javascript" src="/js/webcola/WebCola/cola.min.js"></script> <script type="text/javascript" src="/js/dagre/dist/dagre.min.js"></script> <script type="text/javascript" src="/js/cytoscape-cose-bilkent/cytoscape-cose-bilkent.js"></script> --> <script src="/js/3.42.3/dojo/dojo.js"></script> <script> require(["p3/layer/core"], function(){ require(["p3/app/p3app"], function(App){ appOpts = {"version":"3.0","gaID":"G-GS8F60MG56","uaID":"UA-165638318-1","probModelSeedServiceURL":"https://p3.theseed.org/services/ProbModelSEED","shockServiceURL":"https://p3.theseed.org/services/shock_api","workspaceServiceURL":"https://p3.theseed.org/services/Workspace","appBaseURL":"https://www.bv-brc.org","appServiceURL":"https://p3.theseed.org/services/app_service","dataServiceURL":"https://www.bv-brc.org/api-for-website","homologyServiceURL":"https://p3.theseed.org/services/homology_service","mailinglistURL":"https://lists.brcgateway.org/","genomedistanceServiceURL":"https://p3.theseed.org/services/minhash_service","compareregionServiceURL":"https://www.bv-brc.org/services/compare_regions","docsServiceURL":"https://www.bv-brc.org/docs/","enableDevTools":false,"accountURL":"https://user.bv-brc.org","appLabel":"","jiraLabel":"PROD","appVersion":"3.42.3","userServiceURL":"https://user.bv-brc.org","localStorageCheckInterval":86400}; appOpts.workspaceAPI = "https://p3.theseed.org/services/Workspace"; appOpts.serviceAPI = "https://p3.theseed.org/services/app_service"; appOpts.dataAPI = "https://www.bv-brc.org/api-for-website"; appOpts.userServiceURL = "https://user.bv-brc.org"; appOpts.mailinglistURL = "https://lists.brcgateway.org/"; appOpts.localStorageCheckInterval = "86400"; window.App = new App(appOpts); }); }); </script> <!-- Google Analytics 4 --> <!-- Global site tag (gtag.js) - Google Analytics --> <script async src="https://www.googletagmanager.com/gtag/js?id=G-GS8F60MG56"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'G-GS8F60MG56', { 'link_attribution': true }); </script> <!-- Google UA (EOL) --> <!-- Global site tag (gtag.js) - Google Analytics --> <script async src="https://www.googletagmanager.com/gtag/js?id=UA-165638318-1"></script> <script> window.dataLayer = window.dataLayer || []; function gtag(){dataLayer.push(arguments);} gtag('js', new Date()); gtag('config', 'UA-165638318-1', { 'link_attribution': true }); </script> </body> </html>