KEGG Web Applications

<!DOCTYPE html> <html lang="en"> <head> <meta charset="utf-8"> <meta name="viewport" content="width=device-width, initial-scale=1"> <title>KEGG Web Applications</title> <link rel="stylesheet" href="/css/kegg25.css"> <script src="/js/jquery-3.5.1.min.js"></script> <script src="/kegg/js/launcher.js"></script> <style> td.box { width: 30px; } td.box2 { width: 15px; } </style> </head> <body> <div id="header3"> <div class="logo3"> <a href="/kegg/"><img src="/Fig/keg100G.png" alt="KEGG in Keg"></a> </div> <div class="title"> <h2 class="txt3">KEGG Web Apps</h2> <h5>JavaScript based applications with client-side operations</h5> </div> </div> </div> <div id="sidebar"> <ul> <li><a href="/kegg/mapper/"><b>KEGG Mapper</b></a></li> <li>  <a href="/kegg/mapper/reconstruct.html"><b>Reconstruct</b></a></li> <li>  <a href="/kegg/mapper/search.html"><b>Search</b></a></li> <li>  <a href="/kegg/mapper/color.html"><b>Color</b></a></li> <li>  <a href="/kegg/mapper/join.html"><b>Join</b></a></li> <li>  <a href="/kegg/mapper/mwsearch.html"><b>MWsearch</b></a></li> <li style="margin-top:4px;">  <a href="/kegg/mapper/convert_id.html">Convert ID</a></li> </ul> <ul> <li><span class="current"><b>KEGG Web Apps</b></span></li> <li>  <a href="/kegg/webapp/color_gui.html">Map coloring GUI</a></li> <li>  <a href="/kegg/webapp/color_url.html">Map coloring URL</a></li> </ul> <ul> <li><a href="/kegg/syntax/"><b>KEGG Syntax</b></a></li> <li>  <a href="/kegg/syntax/taxonomy.html">Taxonomy mapping</a></li> <li>  <a href="/kegg/syntax/gnalign.html">Genome alignment</a></li> <li>  <a href="/kegg/syntax/synteny.html">Synteny analysis</a></li> </ul> <ul> <li><a href="/kegg/annotation/"><b>KEGG Annotation</b></a></li> <li>  <a href="/kegg/annotation/ko_assign.html">KO assignment</a></li> <li>  <a href="/kegg/annotation/ann_stat.html">Current statistics</a></li> <li>  <a href="https://www.kegg.jp/blastkoala/">BlastKOALA</a></li> <li>  <a href="https://www.kegg.jp/ghostkoala/">GhostKOALA</a></li> </ul> <ul> <li><a href="/kegg/kegg2.html">KEGG2</a></li> <li><a href="/kegg/">KEGG</a></li> </ul> </div> <div id="content2"> <hr class="frame3" style="margin-top:0;">  <div class="main"> <h4 class="txt3">KEGG Web Apps</h4> <b>KEGG Web Apps</b> are a collection of JavaScript based applications for viewing and analyzing various types of KEGG data with many operations performed on the client side. Currenty they include Pathway viewer for KEGG pathway maps, Brite viewer for Brite hierarchies and Genome browser for genome maps. <br><br> <hr class="frame3"> <h4 class="txt3" id="pathway">Pathway viewer   <span style="font-size:12px; font-weight:normal;">[<a href="/kegg/document/help_pathway.html" target="_blank">Help</a>]</span></h4> <div class="indent"> KEGG pathway map viewer (or Pathway viewer) released in July 2020 [<a href="https://pubmed.ncbi.nlm.nih.gov/33125081">reference</a>] is not simply a viewer, but it contains features of client side operations. All types of KEGG pathway map coloring are now performed on the client side, including the generation of organism-specific pathways except for global maps that are still processed on the server-side, marking of search results and coloring of map objects based on users' data. The viewer can be launched with a simple weblinks form. <div class="indent2"> <a href="https://www.kegg.jp/pathway/map00010">https://www.kegg.jp/pathway/map00010</a> (reference pathway map)<br> <a href="https://www.kegg.jp/pathway/hsa04010">https://www.kegg.jp/pathway/hsa04010</a> (organism-specific pathway map) </div> Default coloring used in KEGG is summarized below for regular maps (boxes) and global/overview maps (lines). See more details in <a href="/kegg/kegg1c.html#mapping">Color codes</a>. <div class="indent2"> <table> <tr> <td>Organism-specific pathway  </td> <td class="box" style="background-color:#bfffbf;"></td> </tr> <tr> <td></td> <td class="center"><span style="color:#00cc33">▬▬</span></td> </tr> <tr> <td>KO/EC/RN pathway</td> <td class="box" style="background-color:#bbccff;"></td> </tr> <tr> <td></td> <td class="center"><span style="color:#3366ff">▬▬</span></td> </tr> </table> <table style="border-collapse:collapse;"> <tr> <td>Two organisms in 3-color  </td> <td class="box" style="background-color:#bfffbf;"></td> <td class="box" style="background-color:#ffbbcc;"></td> <td class="box2" style="background-color:#bbccff;"></td> <td class="box2" style="background-color:#bbccff;"></td> </tr> <tr> <td></td> <td class="center"><span style="color:#00cc33">▬▬</span></td> <td class="center"><span style="color:#ff3366">▬▬</span></td> <td class="center" colspan="2"><span style="color:#3366ff">▬▬</span></td> </tr> <tr><td colspan="5"></td></tr> <tr> <td>Two organisms in split color  </td> <td class="box" style="background-color:#bfffbf;"></td> <td class="box" style="background-color:#ffbbcc;"></td> <td class="box2" style="background-color:#bfffbf;"></td> <td class="box2" style="background-color:#ffbbcc;"></td> </tr> </table> </div> <br> User-defined map coloring methods are described in the following documents. <ul style="list-style:none;"> <li style="padding-bottom:4px;"><a href="/kegg/webapp/color_gui.html"><b>Map coloring GUI</b></a></li> <li><a href="/kegg/webapp/color_url.html"><b>Map coloring URL</b></a></li> </ul> </div> <h4 class="txt3" id="brite">Brite viewer   <span style="font-size:12px; font-weight:normal;">[<a href="/kegg/document/help_brite.html" target="_blank">Help</a>]</span></h4> <div class="indent"> Brite hierarchy viewer (or Brite viewer) released in January 2021 [<a href="https://www.ncbi.nlm.nih.gov/pubmed/34423492">reference</a>] is another web application capable of client side operations such as join and other Brite mapping operations. The viewer can be launched with a simple weblinks form. <div class="indent2"> <a href="https://www.kegg.jp/brite/ko00001">https://www.kegg.jp/brite/ko00001</a> (KO hierarchy)<br> <a href="https://www.kegg.jp/brite/br08611">https://www.kegg.jp/brite/br08611</a> (taxonomy) </div> A special purpose Brite viewer called <b class="txt3">Taxonomy viewer</b> has also been developed for use with <a href="/kegg/syntax/#taxonomy">KEGG taxonomy files</a>. Its main operation is <a href="/kegg/genome/taxonomy.html">taxonomy mapping</a> to examine taxonomic distributions of KOs, modules and other data objects. </div> <h4 class="txt3" id="genome">Genome browser   <span style="font-size:12px; font-weight:normal;">[<a href="/kegg/document/help_genome.html" target="_blank">Help</a>]</span></h4> <div class="indent"> KEGG Genome browser released in January 2022 [<a href="https://pubmed.ncbi.nlm.nih.gov/36300620">reference</a>] is another web application, which integrates server side features of <a href="/kegg/genome/synteny.html">synteny analysis</a> for finding conserved gene orders in multiple genomes. The browser can be launched with a simple weblinks form. <div class="indent2"> <a href="https://www.kegg.jp/genome/T01001">https://www.kegg.jp/genome/T01001</a> (Human genome)<br> <a href="https://www.kegg.jp/genome/hsa">https://www.kegg.jp/genome/hsa</a> (same as above)<br> <a href="https://www.kegg.jp/genome/37296">https://www.kegg.jp/genome/37296</a> (Human gammaherpesvirus 8 genome) </div> The browser is available for the genomes with the NCBI assembly level of "Complete genome" or "Chromosome" as shown in the following brite file. <ul style="list-style:none;"> <li><a href="/brite/br08611">KEGG organisms in taxonomic ranks</a></li> </ul> </div> </div> <br> <hr class="frame3"> <i>Last updated: September 24, 2024</i>  </div> </body> </html>

CINXE.COM

KEGG Web Applications