cgi-bin/about/release_notes/tomato_unigene_build1.pl

   1 use strict;
   2
   3 use CXGN::Page;
   4 use CXGN::Page::FormattingHelpers qw/info_section_html info_table_html/;
   5
   6 my $page=CXGN::Page->new('Tomato Unigene Build 1 Notes','Lukas');
   7 $page->header('tomato unigene build release notes','About the tomato unigene build 1');
   8
   9 print<<END_HEREDOC;
  10
  11 <div class="indentedcontent">
  12
  13 September 2006<br /><br />
  14 A new unigene build for tomato has been assembled from the following data:
  15 <ul>
  16     <li>235836 ESTs from the tomato species
  17     <ul>
  18       <li><i>Solanum lycopersicum</i></li>
  19       <li><i>Solanum habrochaites</i></li>
  20       <li><i>Solanum pennellii</i></li>
  21       <li><i>Microtom.</i></li>
  22     </ul>
  23     We also included 3336 mRNA sequences from Genbank for the
  24     following tomato species:
  25     <ul>
  26       <li><i>Solanum lycopersicum</i></li>
  27       <li><i>Solanum habrochaites</i></li>
  28       <li><i>Solanum pennellii</i></li>
  29       <li><i>Solanum pimpinellifolium</i></li>
  30       <li><i>Solanum peruvianum</i></li>
  31       <li><i>Solanum cheesmaniae</i></li>
  32       <li><i>Solanum habrochaites</i></li>
  33       <li><i>Solanum lycopersicoides</i></li>
  34     </ul>
  35     </li>
  36
  37     <li>New EST sequences were obtained from
  38       <ul>
  39         <li>Prof Shibata, Kazusa Institute.</li>
  40         <li>Dr. Eyal Fridman, University of Michigan</li>
  41       </ul>
  42     </li>
  43
  44     <li>The new build contains 34829 unigenes, of which 21153 are
  45     contigs and 13676 are singletons.</li>
  46
  47     <li>Analyses performed on the unigenes:
  48     <ul>
  49       <li>ESTScan - to predict peptides</li>
  50       <li>InterproScan on peptides - to predict protein domains and
  51       associate Gene Ontology codes</li>
  52       <li>BLAST against Arabidopsis and Genbank NR</li>
  53     </ul>
  54     </li>
  55     <li>The range of unigene ids for this build is: 312296 through 347124.</li>
  56     </ul>
  57 SGN Links:
  58 <ul>
  59 <li><a href="http://sgn-devel.sgn.cornell.edu/search/direct_search.pl?search=unigene">SGN Unigene Search</a></li>
  60 <li><a href="ftp://ftp.sgn.cornell.edu/unigene_builds">SGN FTP server</a></li>
  61 </ul>
  62
  63 External Links:
  64 <ul>
  65 <li><a href="http://www.kazusa.or.jp/jsol/microtom/index.html" class="external">Micro-Tom Database Kazusa, Japan</a></li>
  66 </ul>
  67 </div>
  68
  69 END_HEREDOC
  70
  71 $page->footer();