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GenomeNet
<?xml version="1.0" encoding="UTF-8"?> <!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Transitional//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-transitional.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8" /> <title>GenomeNet</title> <meta name="Keywords" content="GenomeNet, KEGG, DBGET, Kyoto University Bioinformatics Center, Tara Oceans, metagenome, MGENES" /> <meta name="Description" content="GenomeNet is a Japanese network of database and computational services for genome research and related research areas in biomedical sciences." /> <link rel="stylesheet" href="/css/gn_dbget.css" type="text/css" /> </head> <body bgcolor="#ffffff" link="#003399" vlink="#003399"> <table width="720" border="0" cellpadding="0" cellspacing="0"> <tr> <td><a href="/"><img src="/Fig/gn_ttl.gif" alt="transparent" border="0" /></a></td> <th align="right" valign="top"> <a href="/kegg/"><font class="header">KEGG</font></a> <a href="/kegg/kegg2.html"><font class="header">KEGG2</font></a> <a href="/kegg/pathway.html"><font class="header">PATHWAY</font></a> <a href="/kegg/brite.html"><font class="header">BRITE</font></a> <a href="/kegg/medicus.html"><font class="header">MEDICUS</font></a> <a href="/dbget/"><font class="header">DBGET</font></a> <a href="/linkdb/"><font class="header">LinkDB</font></a> </th> </tr> </table> <br /> <table width="720" border="0" cellpadding="10" cellspacing="0"> <tr> <td width="100" rowspan="2" align="center" valign="middle"><a href="/"><img src="/Fig/gntop2.gif" alt="GenomeNet" border="0" /></a></td> <td align="right" valign="top"><font class="header">[ English | <a href="/ja/">Japanese</a> ]</font></td> </tr> <tr> <td valign="top"> <table cellpadding="0" cellspacing="0"> <tr><td nowrap="nowrap"> <form method="get" action="/dbget-bin/www_bfind_sub"> <input type="hidden" name="mode" value="bfind" /> <input type="hidden" name="max_hit" value="1000" /> <b>Search</b> <select name="dbkey"> <option value="alldb" selected="selected">All databases</option> <option value="ontology">Ontology</option> <option value="brite"> KEGG BRITE</option> <option value="go"> GO</option> <option value="pathway_all">Pathway</option> <option value="pathway"> KEGG PATHWAY</option> <option value="module"> KEGG MODULE</option> <option value="network_all">Network</option> <option value="network"> KEGG Network</option> <option value="variant"> KEGG Variant</option> <option value="disease_all">Disease</option> <option value="disease"> KEGG DISEASE</option> <option value="drug_all">Drug</option> <option value="drug"> KEGG DRUG</option> <option value="dgroup"> KEGG DGROUP</option> <option value="ligandbox"> LigandBox</option> <option value="sider"> SIDER</option> <option value="substance_all">Chemical substance</option> <option value="compound"> KEGG COMPOUND</option> <option value="glycan"> KEGG GLYCAN</option> <option value="pubchem"> PubChem</option> <option value="chebi"> ChEBI</option> <option value="pdb-ccd"> PDB-CCD</option> <option value="lipidmaps"> LIPIDMAPS</option> <option value="knapsack"> KNApSAcK</option> <option value="hmdb"> HMDB</option> <option value="reaction_all">Chemical reaction</option> <option value="enzyme"> KEGG ENZYME</option> <option value="reaction"> KEGG REACTION</option> <option value="rclass"> KEGG RCLASS</option> <option value="genome_all">Genome</option> <option value="genome"> KEGG GENOME</option> <option value="mgenome"> KEGG MGENOME</option> <option value="genes_all">Gene</option> <option value="orthology"> KEGG ORTHOLOGY</option> <option value="genes"> KEGG GENES</option> <option value="mgenes"> KEGG MGENES</option> <option value="refgene"> RefGene</option> <option value="ncbi-gene"> NCBI-Gene</option> <option value="ensembl"> Ensembl</option> <option value="hgnc"> HGNC</option> <option value="brc-dna"> RIKEN BRC-DNA</option> <option value="aaseq_all">Protein sequence</option> <option value="uniprot"> UniProt</option> <option value="refpep"> RefSeq</option> <option value="ntseq_all">DNA sequence</option> <option value="refnuc"> RefSeq</option> <option value="dna-today-nonst"> INSDC</option> <option value="structure_all">3D Structure</option> <option value="pdb"> PDB</option> <option value="motifdic">Protein domain</option> <option value="interpro"> InterPro</option> <option value="pfam"> Pfam</option> <option value="prosite"> PROSITE</option> <option value="expression">Gene expression</option> <option value="expression"> EXPRESSION</option> </select> <b>for</b> <input type="text" size="40" name="keywords" /> <input type="submit" value="Go" /> <input type="reset" value="Clear" /> </form> <br /> </td></tr> </table> <!-- <span style="font-weight:bold;color:red;"> Due to network maintenance, brief service interruptions will occur sometime between 04:30-06:00 on Saturday, 15 June (JST). Sorry for the inconvenience.</span><br><br> --> </td> </tr> </table> <table width="720" border="0" cellpadding="0" cellspacing="0"> <tr><td colspan="3"><img src="/Fig/gn_line.gif" alt="line" /></td></tr> <tr valign="top"><td width="140" class="td60"> <table border="0" cellspacing="4" cellpadding="4"> <tr><td></td></tr> <tr><td><font class="current"><b>GenomeNet</b></font><br /> <a href="/en/about.html">About GenomeNet</a><br /> <a href="/en/release.html">Release notes</a><br /> <a href="/en/acknowledge.html">Acknowledgments</a></td></tr> <tr><td><a href="/en/gn_dbget.html"><b>DBGET</b></a><br /> <a href="/en/about_dbget.html">Overview</a><br /> <a href="/en/info_dbget.html">DB release info</a></td></tr> <tr><td><a href="http://www.kegg.jp/"><b>KEGG</b></a></td></tr> <tr><td><a href="/en/gn_orfdb.html"><b>Community DBs</b></a></td></tr> <tr><td><a href="/en/gn_tools.html"><b>Bioinformatics tools</b></a><br /> <!-- <a href="/en/gn_kubic.html">Other tools</a></td></tr>--> <tr><td><a href="/en/gn_ftp.html"><b>FTP</b></a></td></tr> <tr><td><a href="http://www.genome.jp/feedback/"><b>Feedback</b></a></td></tr> </table> </td><td width="20"></td><td width="560"> <!-- start --> <br /> <table><tr valign="top"><td width="300"> <table> <tr><td> <h3 class="title6">GenomeNet Database Resources</h3> <a href="/en/gn_dbget.html"><b>DBGET</b></a>: Integrated Database Retrieval System<br /> <a href="/dbget/">DBGET search</a><br /> <a href="/linkdb/">LinkDB search</a> <a href="/linkdb/linkdb_rdf.html">SPARQL endpoint available</a> </td></tr> <tr><td> <a href="/kegg/"><b>KEGG</b></a>: Kyoto Encyclopedia of Genes and Genomes<br /> <a href="/kegg/kegg2.html">KEGG2</a> - Table of contents<br /> <a href="/kegg/pathway.html">KEGG PATHWAY</a> - Systems information: pathways<br /> <a href="/kegg/brite.html">KEGG BRITE</a> - Systems information: ontologies<br /> <a href="/kegg/catalog/org_list.html">KEGG Organisms</a> - Organism-specific entry points<br /> <a href="/kegg/genes.html">KEGG GENES</a> - Genomic information<br /> <a href="/kegg/ligand.html">KEGG LIGAND</a> - Chemical information<br /> <a href="/kegg/medicus.html">KEGG MEDICUS</a> - Health information </td></tr> <tr><td> <a href="/mgenes/"><b>KEGG MGENES</b></a>: Metagenome gene catalogs </td></tr> <tr><td> <a href="/tools/oc/"><b>KEGG OC</b></a> - KEGG ortholog clusters<br /> <a href="/tools/gn_ga_tools_api.html">REST service is available</a><br /> <a href="/oc/">SPARQL endpoint available</a> </td></tr> <tr><td> <a href="/virushostdb/"><b>Virus-Host DB</b></a>: Hosts of sequenced viruses <!-- span style="font-weight:bold;color:red;">(Under maintenance)</span --> </td></tr> <tr><td> <a href="/taxonomy/"><b>Taxonomy</b></a>: Organism classification </td></tr> <tr><td> <a href="/reaction/"><b>Reaction Ontology</b></a>: Reaction classifications </td></tr> <tr><td> <a href="http://www.vardb.org/"><b>varDB</b></a>: Antigenic variation database </td></tr> <!-- <tr><td> <a href="/en/gn_orfdb.html"><b>Community Databases</b></a><br /> <a href="http://cyano.genome.ad.jp/">CYORF</a> - Cyanobacteria annotation database<br /> <a href="http://bacillus.genome.ad.jp/">BSORF</a> - Bacillus subtilis genome database<br /> <a href="/kegg/expression/">EXPRESSION</a> - Gene expression profile database<br /> <a href="/dbget/org_list2.html">EST (EGENES)</a> - Genomes from EST Datasets </td></tr>--> <tr><td> <h3 class="title6"><a href="/en/gn_tools.html">GenomeNet Bioinformatics Tools</a></h3> <b class="title6">Sequence Analysis</b><br /> <a href="/tools/blast/">BLAST</a> / <a href="/tools/fasta/">FASTA</a> - Sequence similarity search<br /> <!--- <a href="http://dev.genome.jp/tools/ghostx/">GHOSTX is available</a><br /> ---> <a href="/tools/motif/">MOTIF</a> - Sequence motif search<br /> <a href="/tools/mafft/">MAFFT</a> / <a href="/tools/clustalw/">CLUSTALW</a> / <a href="/tools/prrn/">PRRN</a> - Multiple alignment<br /> <a href="/tools/ete/">TREE</a> - Phylogenetic analysis </td></tr> <tr><td style="white-space:nowrap"> <b class="title6">Genome Analysis</b><br /> <a href="/digalign/">DiGAlign</a> - The Dynamic Genomic Alignment Server <!-- span style="font-weight:bold;color:red;">(Under maintenance)</span --><br /> <a href="/viptree/">ViPTree</a> - The Viral Proteomic Tree Server <!--span style="font-weight:bold;color:red;">(Under maintenance)</span --><br /> <!-- <a href="/tools/gn_ga_tools_api.html">REST service is available</a><br />--> <a href="/tools/kofamkoala/">KofamKOALA</a> - Gene annotation and KEGG mapping <!-- font class="new">New!</font --><br /> <a href="/tools/kaas/">KAAS</a> - KEGG automatic annotation server<br /> <!-- <a href="/tools/maple/">MAPLE 2.3</a> - Functionome evaluator<br /> (<a href="/tools/maple21/">MAPLE 2.1</a>)<br /> --> <a href="/tools/egassembler/">EGassembler</a> - EST consensus contigs<br /> <a href="/tools/genies/">GENIES</a> - Gene network prediction<br /> <a href="/tools/dinies/">DINIES</a> - Drug-target network prediction </td></tr> <tr><td> <b class="title6">Chemical Analysis</b><br /> <a href="/tools/simcomp/">SIMCOMP</a> / <a href="/tools/subcomp/">SUBCOMP</a> - Chemical structure search<br /> <a href="/tools/gn_ca_tools_api.html">REST service is available</a><br /> <a href="/tools/kcam/">KCaM</a> - Glycan structure search<br /> <a href="/tools/pathcomp/">PathComp</a> - Possible reaction path computation<br /> <a href="/tools/pathsearch/">PathSearch</a> - Similar reaction path search<br /> <a href="/tools/pathpred/">PathPred</a> - Reaction pathway prediction<br /> <a href="/tools/e-zyme/">E-zyme</a> - Enzymatic reaction prediction </td></tr> </table> </td><td> <br /><br /> <!-- <table cellspacing="10" cellpadding="10"><tr><td class="td60"> <a href="/kegg-bin/get_htext?br08902.keg">BRITE Functional Hierarchies</a><br /> <a href="/kegg-bin/get_htext?br08901.keg">KEGG Pathway Maps</a><br /> <a href="/kegg-bin/get_htext?br08601.keg">KEGG Organisms</a><p /> Genome Catalogs</a><br /> <a href="/kegg/catalog/org_list.html">Complete (KEGG GENES)</a><br /> <a href="/kegg/catalog/org_list3.html">Meta (KEGG MGENES)</a><br /> <a href="/en/gn_ftp.html">FTP download</a></br> <a href="/kegg-bin/get_htext?Viruses+-e">Viral (Viruses)</a><br />--> <!-- <a href="/dbget/org_list2.html">EST (EGENES)</a><p /> --> <!--<a href="/tools/oc/">Ortholog Clusters (OC)</a><br /> </td></tr></table>--> <br /> <table cellspacing="5" cellpadding="5"><tr><td align="center"> <table cellpadding="0"> <tr><td> <a href="/linkdb/"><img src="/Fig/LinkDB_with_logo.png" width="220" alt="LinkDB" border="0" /></a> </td></tr> </table> <a href="/linkdb/">Database links</a> </td></tr></table> <br /> <table cellspacing="5" cellpadding="5"><tr><td align="center"> <table cellpadding="0"> <tr><td> <!--<a href="http://www.kanehisa.jp/en/db_growth.html"><img src="/Fig/db_growth.gif" alt="DB growth curve" border="0" /></a>--> <a href="http://www.kanehisa.jp/en/db_growth.html"><img src="/Fig/db_growth.gif" width="220" alt="DB growth curve" border="0" /></a> </td></tr> </table> <a href="http://www.kanehisa.jp/en/db_growth.html">DB growth curve</a> </td></tr></table> </td></tr></table> <br /> <!-- end --> </td></tr> <tr><td colspan="3"><img src="/Fig/gn_line.gif" alt="line" /></td></tr> </table> <table width="720" border="0" cellpadding="4" cellspacing="4"> <tr><td align="center"><font class="header"><a href="http://www.bic.kyoto-u.ac.jp/">Kyoto University Bioinformatics Center</a></font></td></tr> </table> </body> </html>