cgi-bin/markers/cos_markers.pl

   1 use strict;
   2 use CXGN::Page;
   3 my $page=CXGN::Page->new('cos_markers.html','html2pl converter');
   4 $page->header('Conserved Ortholog Set (COS) markers');
   5 print<<END_HEREDOC;
   6
   7   <center>
   8
   9
  10     <table summary="" width="720" cellpadding="0" cellspacing="0"
  11     border="0">
  12       <tr>
  13         <td>
  14           <center>
  15             <h3>Conserved Ortholog Set (COS) markers</h3>
  16           </center>
  17
  18           <p>We have used a computational method to screen the
  19           tomato EST database against the arabidopsis genome
  20           sequence in order to find a set of highly conserved,
  21           single copy genes which can be used as markers for
  22           comparative mapping between the tomato and arabidopsis
  23           genomes. Currently we have identified approximately 1000
  24           of these Conserved Ortholog Set (COS) markers.<br /></p>
  25
  26           <p>In this section of SGN, you will find sequence and
  27           clone information for each of these COS markers as well
  28           as their matching counterpart in the arabidopsis genome.
  29           We have surveyed these COS markers and mapped some of
  30           these COS markers on the tomato genome to provide a
  31           tomato: arabidopsis comparative map. This mapping
  32           information is available on SGN now.<br /></p>
  33
  34           <p>Because these COS markers are so highly conserved,
  35           they may also be useful for comparative mapping in other
  36           dicot species. The computational screen by how COS
  37           markers were identified is described below:</p>
  38
  39           <ul>
  40             <li>TBLASTX tomato ESTs against the arabidopsis genome
  41             (specifically, the BAC tiling path from TAIR)</li>
  42
  43             <li>Identify single best matches (&lt; e -15) between a
  44             single tomato EST (or associated contig) and a single
  45             BAC in Arabidopsis. Each tomato EST must pass the
  46             following criteria:
  47
  48               <ul>
  49                 <li>it hits an arabidopsis sequence at a
  50                 significance level of &lt; e -15</li>
  51
  52                 <li>it is determined to be NOT part of a domain
  53                 (where several solanaceous sequences hit the same
  54                 arabidopsis region)</li>
  55
  56                 <li>the next best Arabidopsis hit must be of lower
  57                 significance (delta e &gt; 10)</li>
  58               </ul>
  59             </li>
  60
  61             <li>ESTs that pass all these criteria are classified as
  62             conserved orthologs, all others are considered
  63             potentially paralogous and eliminated.</li>
  64           </ul><br />
  65
  66           <h4>Functional annotation of COS markers</h4>
  67
  68           <p>COS-markers were functionally annotated using the MIPS
  69           role categories as they were defined at the time of the
  70           analysis. As the functional role descriptions are subject
  71           to continued changes, a copy of the role categories and
  72           the COS-marker annotations as used in the analysis can be
  73           found below:<br /></p>
  74
  75           <p><a href="/documents/markers/role_categories.txt">MIPS role categories at
  76           time of COS marker annotation</a></p>
  77
  78           <h4>The list of COS markers is available in both online
  79           and plain text format</h4>
  80
  81           <p><a href="/search/markers/cos_list.pl">COS list
  82           online</a> - online format with links to sequences and
  83           tiling path.<br />
  84           <a href="/documents/markers/cos_list-old.txt">Old plain text download</a> - plain
  85           text format for download. <br />
  86           <a href="/documents/markers/cos_list.txt">Old plain text download 2</a> - plain
  87           text format for download.
  88           </p>
  89
  90           <p><strong>Note:</strong> for the tomato map position in
  91           the table linked above:</p>
  92
  93           <ul>
  94             <li>Copy No is how many copies the COS marker shows on
  95             a southern blot survey- S(single) is 1-2 copy, L(low)
  96             is 3-4 copy, M(multiple) means more than 4 copy.</li>
  97
  98             <li>Map position is where the COS marker mapped on the
  99             tomato: arabidopsis systeny map. For example, T1675 map
 100             position is 01.005, meaning Chromosome 1, 5 cM down
 101             from the top. Most of the COS markers have only one map
 102             position, if the COS marker has a second or third map
 103             position, then there were two or three alleles that
 104             could be mapped.</li>
 105           </ul><br />
 106           <br />
 107         </td>
 108       </tr>
 109     </table>
 110
 111   </center>
 112 END_HEREDOC
 113 $page->footer();