cgi-bin/markers/microsats.pl

   1 use strict;
   2 use CXGN::Page;
   3 my $page=CXGN::Page->new('microsats.html','html2pl converter');
   4 $page->header('Microsatellites (SSRs)');
   5 print<<END_HEREDOC;
   6
   7   <center>
   8
   9     <br />
  10
  11     <h3 align="center">Microsatellites (SSRs)</h3>
  12
  13     <p>While microsatellites or simple sequence repeats (SSRs)
  14     normally occur in non-coding regions of the genome, they can
  15     also occur in either 3' or 5' UTRs of ESTs or even in coding
  16     regions (usually triplet repeats). For this reason, the tomato
  17     and potato EST sequences contained in SGN were screened for
  18     microsatellite sequence motifs in May 2001 using analytical
  19     tools developed by Genomics Edge Technologies, Inc; St. Louis,
  20     Missouri. The purpose was to identify SSRs that might be useful
  21     a polymorphic molecular markers genetic and breeding studies in
  22     tomato. The search parameters were for all possible repeat
  23     motifs 2 bp to 6 bp with repeat blocks &gt; 20 bp. The search
  24     algorithms allowed for imperfect repeats as well as complex
  25     repeats.</p>
  26
  27     <p>For those wishing to test SSRs for mapping/polymorphism
  28     studies, it is recommended (based on empirical testing) to start
  29     with:<br /></p>
  30
  31     <ul>
  32       <li>dinucleotides &gt; 12 repeats</li>
  33
  34       <li>trinucleotide &gt; 8 repeats</li>
  35
  36       <li>tetra to hexonuclotides &gt; 6 repeats</li>
  37     </ul>
  38     <p>
  39     <a href="/search/markers/markersearch.pl?searchtype=startswith&amp;name=&amp;submit=search&amp;mapped=on&amp;confidence=0&amp;offsetstart=&amp;offsetend=&amp;chromosomes=all&amp;species=all&amp;maps=all&amp;types=SSR&amp;techniques=all">See all SSR markers in marker search results</a><br />
  40     <a href="/documents/markers/microsat_list.txt">Old text version SSR list</a>
  41     </p>
  42
  43   </center>
  44 END_HEREDOC
  45 $page->footer();