cgi-bin/about/release_notes/tomato_unigene_build2.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 2 Notes','Lukas');
   7 $page->header('tomato unigene build release notes','About the tomato unigene build 2');
   8
   9 print<<END_HEREDOC;
  10
  11 <div class="indentedcontent">
  12
  13 May 2008<br /><br />
  14 A new unigene build for tomato has been assembled from the following data:
  15 <ul>
  16     <li>323,277 ESTs from the tomato species
  17     <ul>
  18       <li><i>Solanum lycopersicum</i> with 307,350 sequences</li>
  19       <li><i>Solanum habrochaites</i> with 8,255 sequences</li>
  20       <li><i>Solanum pennellii</i> with 7,812 sequences</li>
  21       <li><i>Solanum pimpinellifolium</i> with 8 sequences</li>
  22       <li><i>Solanum peruvianum</i> with 42 sequences</li>
  23       <li><i>Solanum cheesmaniae</i> with 4 sequences</li>
  24       <li><i>Solanum lycopersicoides</i> with 2 sequences</li>
  25     </ul>
  26     </li>
  27
  28     <li>New EST sequences were obtained from:
  29       <ul>
  30         <li>GenBank database (dbEST and mRNA for nucleotide)</li>
  31       </ul>
  32     </li>
  33
  34     <li>The new build contains 42,257 unigenes, of which 24,020 are
  35     contigs and 18,237 are singletons.</li>
  36
  37     <li>Analyses performed on the unigenes:
  38     <ul>
  39       <li>ESTScan and Longest6frame.pl - to predict peptides (39,967
  40       and 43,366 peptides predicted respectively)</li>
  41       <li>InterproScan on peptides - to predict protein domains and
  42       associate Gene Ontology codes (6,626 and 1,482 different domains
  43       associated to the two different peptide datasets from the two different
  44       peptide prediction methods)</li>
  45       <li>BLAST against Genbank NR, Arabidopsis and Swissprot (30,791, 28,656 and 19,886 unigenes have
  46       any match with these protein datasets respectively)</li>
  47     </ul>
  48     </li>
  49     <li>The range of unigene ids for this build is: SGN-U562593 through SGN-U604849.</li>
  50     </ul>
  51
  52 Different ways to access to new tomato species unigene build in SGN:
  53 <ul>
  54 <li>Sequence homology search using <a href="http://sgn.cornell.edu/tools/blast/">SGN Blast</a>.</li>
  55 <li>Bulk download for a unigene accession (or list of accessions)
  56 using SGN <a href="http://sgn.cornell.edu/bulk/input.pl?mode=unigene">Bulk download tool</a>.</li>
  57 <li>Complete download of all the unigene sequences and annotations from
  58 the <a href="ftp://ftp.sgn.cornell.edu/unigene_builds">SGN ftp site</a>.</li>
  59
  60 </div>
  61
  62 END_HEREDOC
  63
  64 $page->footer();