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<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>
</table>
<center>
<H1><center>TyrA Subsystem</center></H1>
<table class=ft border:0 cellpadding=10 cellspacing=10 width="80%">
<tr>
<td width=350>
<img src=./arrow.jpg> <strong><a href=tyrACGTree.html>TyrA CG Tree</a></strong></img>
<p> <a href=TyrARep.html>TyrA CG Representative Table</a></p>
<p> <a href=TyrAExtended.html>TyrA CG Extended Table</a></p>
<p> <a href=../tyra_sequence.cgi?group=CG1>TyrA Trimmed Catalytic-core Sequences</a></p>
<img src=./arrow.jpg> <strong><a href=TyrAPanels.html>TyrA CHARACTER-STATE SNAPSHOTS</a></strong></img>
<p>
<img src=./arrow.jpg> <strong>LINKS</strong></img>
<p> <a href=http://aropath.lanl.gov/> AroPath</a>
<p>
<img src=./arrow.jpg> <strong>PUBLICATIONS</strong></img>
<p>
<img src=./arrow.jpg> <strong>AUTHORS</strong> </img>
<p>
<img src=./arrow.jpg> <strong>ACKNOWLEDMENTS</strong></img>
</td>
<td>
<div style='text-align:justify;'>
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>
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>
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<script src="css/FIG.js" type="text/javascript"></script>
</head>
<table width="100%" 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>
</table>
<center>
<H1><center>TyrA Subsystem</center></H1>
<table class=ft border:0 cellpadding=10 cellspacing=10 width="80%">
<tr>
<td width=350>
<img src=./arrow1.jpg> <strong><a href=tyrACGTree.html>TyrA CG Tree</a></strong></img>
<p> <a href=TyrARep.html>TyrA CG Representative Table</a></p>
<p> <a href=TyrAExtended.html>TyrA CG Extended Table</a></p>
<p> <a href=../tyra_sequence.cgi?group=CG1>TyrA Trimmed Catalytic-core Sequences</a></p>
<img src=./arrow1.jpg> <strong><a href=TyrAPanels.html>TyrA CHARACTER-STATE SNAPSHOTS</a></strong></img>
<p>
<img src=./arrow1.jpg> <strong>LINKS</strong></img>
<p> <a href=http://aropath.lanl.gov/> AroPath</a>
<p>
<img src=./arrow1.jpg> <strong>PUBLICATIONS</strong></img>
<p>
<img src=./arrow1.jpg> <strong>AUTHORS</strong> </img>
<p>
<img src=./arrow1.jpg> <strong>ACKNOWLEDMENTS</strong></img>
</td>
<td>
<div style='text-align:justify;'>
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>
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>
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