Parent Directory
| 
Revision Log
Revision 1.9 - (view) (download) (as text)
| 1 : | disz | 1.8 | <html> |
| 2 : | <style> | ||
| 3 : | <!-- | ||
| 4 : | a {text-decoration: none} | ||
| 5 : | a:hover{text-decoration:underline;color:#be0505;} | ||
| 6 : | ul {margin-top: 5px; margin-bottom: 5px;} | ||
| 7 : | p {margin: 10px; margin-left: 1px;} | ||
| 8 : | .ft {border-top: solid #FF0000; | ||
| 9 : | border-bottom: solid #FF0000;} | ||
| 10 : | .ta {text-align:center} | ||
| 11 : | |||
| 12 : | --> | ||
| 13 : | </style> | ||
| 14 : | |||
| 15 : | <link rel='stylesheet' title='default' href='css/default.css' type='text/css'> | ||
| 16 : | <link rel='alternate stylesheet' title='Sans Serif' href='css/sanserif.css' type='text/css'> | ||
| 17 : | <link rel='alternate' title='SEED RSS feeds' href='rss/SEED.rss' type='application/rss+xml'> | ||
| 18 : | <script src="css/FIG.js" type="text/javascript"></script> | ||
| 19 : | </head> | ||
| 20 : | <center> | ||
| 21 : | <table cellspacing=2> | ||
| 22 : | <tr> | ||
| 23 : | <td bgcolor="lightblue"> | ||
| 24 : | <b><font size="+3" >The SEED: an Annotation/Analysis Tool Provided by <a href="FIG.html">FIG</a></font></b> | ||
| 25 : | |||
| 26 : | <br> | ||
| 27 : | disz | 1.9 | [ |
| 28 : | <a href="../index.cgi">The SEED</a> | | ||
| 29 : | <a href="http://subsys.info">Subsystem Forum</a> | | ||
| 30 : | disz | 1.8 | <a href="../eggs.cgi">Essentiality Data</a> | |
| 31 : | <a href="tutorials.html">FIG Tutorials</a> | | ||
| 32 : | <a href="../p2p/new_seed_update_page.cgi?user=">Peer-to-peer Updates</a> | | ||
| 33 : | <a href="../p2p/ch.cgi?user=">(New) Clearinghouse</a> | | ||
| 34 : | |||
| 35 : | <a href="../seed_ctl.cgi?user=">SEED Control Panel</a> | | ||
| 36 : | <a href="http://www.nmpdr.org/">NMPDR</a> | | ||
| 37 : | <a href="http://www-unix.mcs.anl.gov/SEEDWiki/">SEED Wiki</a>] | ||
| 38 : | <br> | ||
| 39 : | [<a href="http://www.genomesonline.org/">GOLD</a> | | ||
| 40 : | <a href="CompleteSeedGenomes.html">"Complete" Genomes in SEED </a> | | ||
| 41 : | <a href="http://au.expasy.org/">ExPASy</a> | | ||
| 42 : | |||
| 43 : | <a href="http://img.jgi.doe.gov/">IMG</a> | | ||
| 44 : | <a href="http://www.genome.jp/kegg/kegg2.html">KEGG</a> | | ||
| 45 : | <a href="http://www.ncbi.nlm.nih.gov/">NCBI</a> | | ||
| 46 : | <a href="http://www.tigr.org/tigr-scripts/CMR2/CMRGenomes.spl">TIGR cmr</a> | | ||
| 47 : | <a href="http://www.pir.uniprot.org/">UniProt</a> | | ||
| 48 : | <a href="http://borrelia.ci.uchicago.edu/fogbugz">Report "Bugz"</a>] | ||
| 49 : | |||
| 50 : | <br> | ||
| 51 : | <br> | ||
| 52 : | <td> | ||
| 53 : | <img src=seed-logo-green.png alt=seedlogo> | ||
| 54 : | </td> | ||
| 55 : | </tr> | ||
| 56 : | </table> | ||
| 57 : | </center> | ||
| 58 : | <center> | ||
| 59 : | <H1><center>TyrA Subsystem</center></H1> | ||
| 60 : | <table class=ft cellspacing=10> | ||
| 61 : | <tr> | ||
| 62 : | <td width=20%> | ||
| 63 : | Mozilla Firefox is recommended as the browser to give the best performance in accessing the links below. | ||
| 64 : | <p> | ||
| 65 : | <img src=./arrow1.jpg> <strong><a href=tyrACGTree.html>TyrA COHESION GROUP (CG) TREE</a></strong></img> | ||
| 66 : | <p> <a href=TyrARep.html>Sources of Representative CG Sequences</a></p> | ||
| 67 : | <p> <a href=TyrAExtended.html>TyrA CG Extended Table</a></p> | ||
| 68 : | <p> <a href=../tyra_sequence.cgi?group=CG1>TyrA Trimmed Catalytic-core Sequences</a></p> | ||
| 69 : | <img src=./arrow1.jpg> <strong><a href=TyrAPanels.html>TyrA CHARACTER-STATE SNAPSHOTS</a></strong></img> | ||
| 70 : | |||
| 71 : | <p> | ||
| 72 : | <img src=./arrow1.jpg> <strong>LINKS</strong></img> | ||
| 73 : | <p> <a href=http://aropath.lanl.gov/> AroPath</a> | ||
| 74 : | <p> | ||
| 75 : | <img src=./arrow1.jpg> <strong>PUBLICATIONS</strong></img> | ||
| 76 : | <p> | ||
| 77 : | <img src=./arrow1.jpg> <strong>AUTHORS</strong> </img> | ||
| 78 : | <p> | ||
| 79 : | <img src=./arrow1.jpg> <strong>ACKNOWLEDMENTS</strong></img> | ||
| 80 : | |||
| 81 : | </td> | ||
| 82 : | <td width=30%> | ||
| 83 : | <div style='text-align:justify;'> | ||
| 84 : | The limitation in genome analysis is not | ||
| 85 : | the availability of sequence data, but rather the interpretation of those | ||
| 86 : | data. Errors in current annotations are abundant. Since new annotations | ||
| 87 : | often rely upon the existing set of annotations, errors have proliferated | ||
| 88 : | and continue to proliferate. The situation is sufficiently severe that in | ||
| 89 : | many cases only experts familiar with particular pathways can recognize | ||
| 90 : | and sort out errors. A major problem has been the untidy and erratic nomenclature | ||
| 91 : | used to identify genes, <i>e.g.,</i><span style='font-style:normal'> | ||
| 92 : | (i) use of the same name for different genes, (ii) use of the same name | ||
| 93 : | for genes that, on the one hand, encode single-domain proteins, and, on | ||
| 94 : | the other hand, genes that encode multi-domain proteins (due to gene fusion), | ||
| 95 : | and (iii) use of different names in different organisms for genes encoding | ||
| 96 : | the same protein. It is absolutely critical (and surely inevitable) that a | ||
| 97 : | logical and consistent universal nomenclature be established.<o:p></o:p></span></p> | ||
| 98 : | The SEED is taking the initiative that | ||
| 99 : | this situation can best be addressed with a comprehensive, expert-assisted | ||
| 100 : | manual effort that is undertaken with a realistically manageable subsystem | ||
| 101 : | of metabolism. No matter how high the quality of an analysis is at a given | ||
| 102 : | time, it will become outdated rapidly as new genomes come on line. | ||
| 103 : | Therefore, our approach is to produce tools which are able to lock in the | ||
| 104 : | current advances in analysis as they come, which are freely available and | ||
| 105 : | interactive so that the previous work can be efficiently exploited, and | ||
| 106 : | which is amenable to progressive updating and refinement via curator | ||
| 107 : | approval at the SEED.<o:p></o:p></p> | ||
| 108 : | </div> | ||
| 109 : | </td> | ||
| 110 : | </tr> | ||
| 111 : | </table> | ||
| 112 : | </center> | ||
| 113 : | </body> | ||
| 114 : | |||
| 115 : | </html> | ||
| 116 : |
| MCS Webmaster | ViewVC Help |
| Powered by ViewVC 1.0.3 |