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Revision 1.9 - (download) (as text) (annotate)
Mon Aug 6 16:05:50 2007 UTC (12 years, 5 months ago) by disz
Branch: MAIN
CVS Tags: rast_rel_2014_0912, rast_rel_2008_06_18, rast_rel_2008_06_16, rast_rel_2008_07_21, rast_rel_2010_0928, rast_2008_0924, rast_rel_2008_09_30, rast_rel_2010_0526, rast_rel_2014_0729, rast_rel_2009_05_18, rast_rel_2009_0925, rast_rel_2010_1206, rast_rel_2010_0118, rast_rel_2009_02_05, rast_rel_2011_0119, rast_rel_2008_12_18, rast_rel_2008_10_09, rast_release_2008_09_29, rast_rel_2008_04_23, rast_rel_2008_08_07, rast_rel_2009_07_09, rast_rel_2010_0827, myrast_33, rast_rel_2011_0928, rast_rel_2008_09_29, rast_rel_2008_10_29, rast_rel_2009_03_26, rast_rel_2008_11_24, HEAD
Changes since 1.8: +3 -1 lines
Added SEED link

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<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>
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<td bgcolor="lightblue">
<b><font size="+3" >The SEED: an Annotation/Analysis Tool Provided by <a href="FIG.html">FIG</a></font></b>

<a href="../index.cgi">The SEED</a> |
<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>]
[<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>]

<img src=seed-logo-green.png alt=seedlogo>
<H1><center>TyrA Subsystem</center></H1>
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Mozilla Firefox is recommended as the browser to give the best performance in accessing the links below.
    <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>Sources of Representative  CG Sequences</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>

    <img src=./arrow1.jpg>&nbsp;<strong>LINKS</strong></img>
       <p>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;<a href=http://aropath.lanl.gov/> AroPath</a>
    <img src=./arrow1.jpg>&nbsp;<strong>PUBLICATIONS</strong></img>
    <img src=./arrow1.jpg>&nbsp;<strong>AUTHORS</strong> </img>
    <img src=./arrow1.jpg>&nbsp;<strong>ACKNOWLEDMENTS</strong></img>
     <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>


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