cgi-bin/methods/unigene/unigene-process-2.pl

   1 use strict;
   2 use CXGN::Page;
   3 my $page=CXGN::Page->new('unigene-process-2.html','html2pl converter');
   4 $page->header('SGN Assembly Process Version 2');
   5 print<<END_HEREDOC;
   6
   7   <center>
   8
   9     <table summary="" width="720" cellpadding="0" cellspacing="0"
  10     border="0">
  11       <tr>
  12         <td>
  13
  14
  15           <h3>SGN Assembly Process Version 2</h3>
  16
  17           <p>ESTs are preclustered using a custom developed tool to
  18           coarsely identify strong sequence overlaps. (<a href=
  19           "unigene-precluster.pl">Why precluster?</a>) This
  20           produces a set of pairwise scores to be used in <a href=
  21           "unigene-precluster.pl">transitive closure
  22           clustering</a>, implemented as a graph algorithm using
  23           depth-first search.</p>
  24
  25           <p>In graph theoretic terms, the sequences are considered
  26           nodes of a graph. Undirected edges between nodes indicate
  27           a detected overlap between the sequences represented by
  28           the nodes. Edges may be weighted, indicating the strength
  29           of the overlap. The connected components of the graph are
  30           discovered by depth first search, yielding a depth first
  31           "forest" of sequence clusters.</p>
  32
  33           <p>Articulation points in the graph are discovered by
  34           analyzing the "tree edge" and "back edge" classification
  35           of edges from depth first search. Nodes identified as
  36           articulation points are potentially chimeric sequences
  37           and their overlaps are analyzed further for adjacent but
  38           distinct homology regions. Sequences with adjacent but
  39           distinct homology regions are considered likely to be
  40           chimeric and are discarded. Since the sequence is an
  41           articulation point, this will break the cluster into two
  42           separate clusters, as expected.</p>
  43
  44           <p>The resulting clusters are supplied as input, with
  45           base calling quality scores, to the <a href=
  46           "http://genome.cs.mtu.edu/cap/cap3.html">CAP3 assembly
  47           program</a>. We have used the following parameters (for
  48           Lycopersicon combined build):</p>
  49
  50           <table summary="" border="1">
  51             <tr>
  52               <td>CAP3 option</td>
  53               <td>default value</td>
  54               <td>value used</td>
  55               <td>description</td>
  56             </tr>
  57
  58             <tr>
  59               <td>-e</td>
  60               <td>30</td>
  61               <td>5000</td>
  62               <td>"extra" number of observed differences</td>
  63             </tr>
  64
  65             <tr>
  66               <td>-s</td>
  67               <td>900</td>
  68               <td>401</td>
  69               <td>minimum similarity score for an overlap</td>
  70             </tr>
  71
  72             <tr>
  73               <td>-p</td>
  74               <td>75</td>
  75               <td>90</td>
  76               <td>percent identity required for overlap</td>
  77             </tr>
  78
  79             <tr>
  80               <td>-d</td>
  81               <td>200</td>
  82               <td>10000</td>
  83               <td>maximum allowed sum of quality scores of
  84               mismatched bases in overlaps</td>
  85             </tr>
  86
  87             <tr>
  88               <td>-b</td>
  89               <td>20</td>
  90               <td>60</td>
  91               <td>quality score threshold for scoring a base
  92               mismatch</td>
  93             </tr>
  94           </table>
  95
  96           <p>Please see the documentation for CAP3 for further
  97           information on other parameters (which are left to
  98           default values) and complete descriptions of the
  99           above.</p>
 100
 101           <p>The point here is to restrict or eliminate the effect
 102           of the "-e, -s, -d, and -b" options, leaving "-p" in the
 103           driver's seat. This makes the decisions to assemble or
 104           not assemble easily interpretable. The other parameters
 105           are attempts to introduce more sensitive discriminations
 106           than just percent identity of a detected overlap.
 107           However, our experience has shown the effects of these
 108           parameters (at default or similar settings) yield
 109           arbitrary assemblies that dominate over the most
 110           intuitive measure, the percent identity in an overlap.
 111           Preliminary experiments indicate that "-p" is the most
 112           useful option for controlling CAP3's behavior, but its
 113           effects are only noticeable when the other overlap
 114           assessment features (options) are effectively
 115           disabled.</p>
 116         </td>
 117       </tr>
 118
 119     </table>
 120   </center>
 121 END_HEREDOC
 122 $page->footer();