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 <html> <style> <!-- a {text-decoration: none} a:hover{text-decoration:underline;color:#be0505;} ul {margin-top: 5px; margin-bottom: 5px;} p {margin: 10px; margin-left: 1px;} .ft {border-top: solid #FF0000;     border-bottom: solid #FF0000;} .ta {text-align:center} --> </style> <link rel='stylesheet' title='default' href='css/default.css' type='text/css'> <link rel='alternate stylesheet' title='Sans Serif' href='css/sanserif.css' type='text/css'> <link rel='alternate'  title='SEED RSS feeds' href='rss/SEED.rss' type='application/rss+xml'> <script src="css/FIG.js" type="text/javascript"></script> </head> <center> <table  cellspacing=2> <tr> <td bgcolor="lightblue"> <b><font size="+3" >The SEED: an Annotation/Analysis Tool Provided by <a href="FIG.html">FIG</a></font></b> <br> [ <a href="http://subsys.info">Subsystem Forum</a> | <a href="../eggs.cgi">Essentiality Data</a> | <a href="tutorials.html">FIG Tutorials</a> | <a href="../p2p/new_seed_update_page.cgi?user=">Peer-to-peer Updates</a> | <a href="../p2p/ch.cgi?user=">(New) Clearinghouse</a> | <a href="../seed_ctl.cgi?user=">SEED Control Panel</a> | <a href="http://www.nmpdr.org/">NMPDR</a> | <a href="http://www-unix.mcs.anl.gov/SEEDWiki/">SEED Wiki</a>] <br> [<a href="http://www.genomesonline.org/">GOLD</a> | <a href="CompleteSeedGenomes.html">"Complete" Genomes in SEED </a> | <a href="http://au.expasy.org/">ExPASy</a> | <a href="http://img.jgi.doe.gov/">IMG</a> | <a href="http://www.genome.jp/kegg/kegg2.html">KEGG</a> | <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a> | <a href="http://www.tigr.org/tigr-scripts/CMR2/CMRGenomes.spl">TIGR cmr</a> | <a href="http://www.pir.uniprot.org/">UniProt</a> | <a href="http://borrelia.ci.uchicago.edu/fogbugz">Report "Bugz"</a>] <br> <br> <td> <img src=seed-logo-green.png alt=seedlogo> </td> </tr> </table> </center> <center> <H1><center>TyrA Subsystem</center></H1>   <table class=ft cellspacing=10>    <tr>    <td width=20%> Mozilla Firefox is recommended as the browser to give the best performance in accessing the links below. <p>    <img src=./arrow1.jpg>&nbsp;<strong><a href=tyrACGTree.html>TyrA CG Tree</a></strong></img>       <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=TyrARep.html>TyrA CG Representative Table</a></p>       <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=TyrAExtended.html>TyrA CG Extended Table</a></p>       <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=../tyra_sequence.cgi?group=CG1>TyrA Trimmed Catalytic-core Sequences</a></p>    <img src=./arrow1.jpg>&nbsp;<strong><a href=TyrAPanels.html>TyrA CHARACTER-STATE SNAPSHOTS</a></strong></img>    <p>    <img src=./arrow1.jpg>&nbsp;<strong>LINKS</strong></img>       <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=http://aropath.lanl.gov/> AroPath</a>    <p>    <img src=./arrow1.jpg>&nbsp;<strong>PUBLICATIONS</strong></img>    <p>    <img src=./arrow1.jpg>&nbsp;<strong>AUTHORS</strong> </img>    <p>    <img src=./arrow1.jpg>&nbsp;<strong>ACKNOWLEDMENTS</strong></img>        </td>     <td width=30%>     <div style='text-align:justify;'>     &nbsp;&nbsp;&nbsp;The limitation in genome analysis is not     the availability of sequence data, but rather the interpretation of those     data. Errors in current annotations are abundant. Since new annotations     often rely upon the existing set of annotations, errors have proliferated     and continue to proliferate. The situation is sufficiently severe that in     many cases only experts familiar with particular pathways can recognize     and sort out errors. A major problem has been the untidy and erratic nomenclature     used to identify genes, <i>e.g.,</i><span style='font-style:normal'>     (i) use of the same name for different genes, (ii) use of the same name     for genes that, on the one hand, encode single-domain proteins, and, on     the other hand, genes that encode multi-domain proteins (due to gene fusion),     and (iii) use of different names in different organisms for genes encoding     the same protein. It is absolutely critical (and surely inevitable) that a     logical and consistent universal nomenclature be established.<o:p></o:p></span></p>     &nbsp;&nbsp;&nbsp;The SEED is taking the initiative that     this situation can best be addressed with a comprehensive, expert-assisted     manual effort that is undertaken with a realistically manageable subsystem     of metabolism. No matter how high the quality of an analysis is at a given     time, it will become outdated rapidly as new genomes come on line.     therefore, our approach is to produce tools which are able to lock in the     current advances in analysis as they come, which are freely available and     interactive so that the previous work can be efficiently exploited, and     which is amenable to progressive updating and refinement via curator     approval at The SEED.<o:p></o:p></p>     </div>     </td>    </tr>   </table> </center> </body> </html>  
1    <html> <style> <!-- a {text-decoration: none} a:hover{text-decoration:underline;color:#be0505;} ul {margin-top: 5px; margin-bottom: 5px;} p {margin: 10px; margin-left: 1px;} .ft {border-top: solid #FF0000;     border-bottom: solid #FF0000;} .ta {text-align:center} --> </style> <link rel='stylesheet' title='default' href='css/default.css' type='text/css'> <link rel='alternate stylesheet' title='Sans Serif' href='css/sanserif.css' type='text/css'> <link rel='alternate'  title='SEED RSS feeds' href='rss/SEED.rss' type='application/rss+xml'> <script src="css/FIG.js" type="text/javascript"></script> </head> <center> <table  cellspacing=2> <tr> <td bgcolor="lightblue"> <b><font size="+3" >The SEED: an Annotation/Analysis Tool Provided by <a href="FIG.html">FIG</a></font></b> <br> [ <a href="http://subsys.info">Subsystem Forum</a> | <a href="../eggs.cgi">Essentiality Data</a> | <a href="tutorials.html">FIG Tutorials</a> | <a href="../p2p/new_seed_update_page.cgi?user=">Peer-to-peer Updates</a> | <a href="../p2p/ch.cgi?user=">(New) Clearinghouse</a> | <a href="../seed_ctl.cgi?user=">SEED Control Panel</a> | <a href="http://www.nmpdr.org/">NMPDR</a> | <a href="http://www-unix.mcs.anl.gov/SEEDWiki/">SEED Wiki</a>] <br> [<a href="http://www.genomesonline.org/">GOLD</a> | <a href="CompleteSeedGenomes.html">"Complete" Genomes in SEED </a> | <a href="http://au.expasy.org/">ExPASy</a> | <a href="http://img.jgi.doe.gov/">IMG</a> | <a href="http://www.genome.jp/kegg/kegg2.html">KEGG</a> | <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a> | <a href="http://www.tigr.org/tigr-scripts/CMR2/CMRGenomes.spl">TIGR cmr</a> | <a href="http://www.pir.uniprot.org/">UniProt</a> | <a href="http://borrelia.ci.uchicago.edu/fogbugz">Report "Bugz"</a>] <br> <br> <td> <img src=seed-logo-green.png alt=seedlogo> </td> </tr> </table> </center> <center> <H1><center>TyrA Subsystem</center></H1>   <table class=ft cellspacing=10>    <tr>    <td width=20%> Mozilla Firefox is recommended as the browser to give the best performance in accessing the links below. <p>    <img src=./arrow1.jpg>&nbsp;<strong><a href=tyrACGTree.html>TyrA COHESION GROUP (CG) TREE</a></strong></img>       <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=TyrARep.html>Representative Sequences for TyrA CGs</a></p>       <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=TyrAExtended.html>TyrA CG Extended Table</a></p>       <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=../tyra_sequence.cgi?group=CG1>TyrA Trimmed Catalytic-core Sequences</a></p>    <img src=./arrow1.jpg>&nbsp;<strong><a href=TyrAPanels.html>TyrA CHARACTER-STATE SNAPSHOTS</a></strong></img>    <p>    <img src=./arrow1.jpg>&nbsp;<strong>LINKS</strong></img>       <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=http://aropath.lanl.gov/> AroPath</a>    <p>    <img src=./arrow1.jpg>&nbsp;<strong>PUBLICATIONS</strong></img>    <p>    <img src=./arrow1.jpg>&nbsp;<strong>AUTHORS</strong> </img>    <p>    <img src=./arrow1.jpg>&nbsp;<strong>ACKNOWLEDMENTS</strong></img>        </td>     <td width=30%>     <div style='text-align:justify;'>     &nbsp;&nbsp;&nbsp;The limitation in genome analysis is not     the availability of sequence data, but rather the interpretation of those     data. Errors in current annotations are abundant. Since new annotations     often rely upon the existing set of annotations, errors have proliferated     and continue to proliferate. The situation is sufficiently severe that in     many cases only experts familiar with particular pathways can recognize     and sort out errors. A major problem has been the untidy and erratic nomenclature     used to identify genes, <i>e.g.,</i><span style='font-style:normal'>     (i) use of the same name for different genes, (ii) use of the same name     for genes that, on the one hand, encode single-domain proteins, and, on     the other hand, genes that encode multi-domain proteins (due to gene fusion),     and (iii) use of different names in different organisms for genes encoding     the same protein. It is absolutely critical (and surely inevitable) that a     logical and consistent universal nomenclature be established.<o:p></o:p></span></p>     &nbsp;&nbsp;&nbsp;The SEED is taking the initiative that     this situation can best be addressed with a comprehensive, expert-assisted     manual effort that is undertaken with a realistically manageable subsystem     of metabolism. No matter how high the quality of an analysis is at a given     time, it will become outdated rapidly as new genomes come on line.     therefore, our approach is to produce tools which are able to lock in the     current advances in analysis as they come, which are freely available and     interactive so that the previous work can be efficiently exploited, and     which is amenable to progressive updating and refinement via curator     approval at The SEED.<o:p></o:p></p>     </div>     </td>    </tr>   </table> </center> </body> </html>

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