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Doc update
For HTML5, plus MUMmer doc improvements.
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‎docs/Demo.html‎

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<!DOCTYPE HTML>
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<html>
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<html lang="en">
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<head>
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<title>SyMAP Demo</title>
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<meta name="viewport" content="width=device-width, initial-scale=1">
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<link rel="stylesheet" href="style.css">
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</head>
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<body>
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<!------ left side index - customize ----------------------------------------------------->
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<!-- left side index - customize -->
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<div class="sidenav">
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<a href="https://csoderlund.github.io">
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<img src="./img/agcol_logo.gif" alt="AGCoL" style="width: 160px; border:1px solid black; background: white;"></a>
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<a href="#top">Go to top</a>
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</div>
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<!------ right side header and body ----------------------------------------------------->
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<!-- right side header and body -->
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<div class="rightSide">
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<a id="top"></a>
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</table>
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</div>
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<!---------------------------- bulk of page ------------------------------------------->
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<!-- =================== bulk of page ======================== -->
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<div class="main">
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<p>This webpage provides results from the supplied demo, which
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<table class="tx">
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<tr><td>&nbsp;<td><small>Click an image to view a closeup.</small>
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<tr><td style="vertical-align: text-top;">
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The demo that is provided with the SyMAP tarball has the projects <ttx>demo_seq</ttx>, <ttx>demo_seq2</ttx>
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and <ttx>demo_draft</ttx>.
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<p>The project <ttx>demo_draft..demo_seq2</ttx> is created with ordered contigs,
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The demo that is provided with the SyMAP tarball has the projects <span class="ttx">demo_seq</span>, <span class="ttx">demo_seq2</span>
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and <span class="ttx">demo_draft</span>.
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<p>The project <span class="ttx">demo_draft..demo_seq2</span> is created with ordered contigs,
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as described in <a href="#draft">Draft</a>.
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<p>This section discusses the
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<ttx>demo_seq</ttx> to <ttx>demo_seq2</ttx> synteny, which represent complete genome sequences.
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<span class="ttx">demo_seq</span> to <span class="ttx">demo_seq2</span> synteny, which represent complete genome sequences.
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<td><a href="img/demoProjects.png">
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<img src="img/demoProjects.png" alt="demo projects" style="border: 1px solid black; width: 450px"></a>
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</table>
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<p>There are a variety of options, as discussed in
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<a href="SystemHelp.html" class="ext" target="_blank">Pair Parameters</a>.
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The following shows the <ttp>Dot Plot</ttp> and <ttp>Summary</ttp> using the following:
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The following shows the <span class="ttp">Dot Plot</span> and <span class="ttp">Summary</span> using the following:
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<p>
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<ul>
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<li><ttl>Cluster Algo1 (original modified)</ttl> or <ttl>Cluster Algo2 (exon-intron)</ttl>: The second
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<li><span class="ttl">Cluster Algo1 (original modified)</span> or <span class="ttl">Cluster Algo2 (exon-intron)</span>: The second
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is recommended when there is good gene annotation provided.
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<p>
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<li><ttl>Synteny Original</ttl> or <ttl>Synteny Strict</ttl>:
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<li><span class="ttl">Synteny Original</span> or <span class="ttl">Synteny Strict</span>:
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The second is recommended for complete genome sequence; it does not perform well for draft.
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</ul>
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<p>
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<a id="dot"></a>
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<table class="tx">
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<tr><td colspan="2"><ttl>Cluster Algo1 (original modified)</ttl> and <ttl>Synteny Original</ttl>
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<tr><td colspan="2"><span class="ttl">Cluster Algo1 (original modified)</span> and <span class="ttl">Synteny Original</span>
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<tr><td style="vertical-align: text-top;"><a href="img/demoSum.png">
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<img src="img/demoSum.png" alt="demoSum" style="border: 1px solid black; width: 350px"></a>
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<td style="vertical-align: text-top;"><a href="img/demoDotplot.png">
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<img src="img/demoDotplot.png" alt="demoDotplot" style="border: 1px solid black; width: 400px"></a>
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<tr><td colspan="2"><ttl>Cluster Algo2 (exon-intron)</ttl> and <ttl>Synteny Strict</ttl>
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<tr><td colspan="2"><span class="ttl">Cluster Algo2 (exon-intron)</span> and <span class="ttl">Synteny Strict</span>
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<tr><td style="vertical-align: text-top;"><a href="img/demoSum2.png">
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<img src="img/demoSum2.png" alt="demo Sum algo2" style="border: 1px solid black; width: 350px"></a>
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<td style="vertical-align: text-top;"><a href="img/demoDotplot2.png">
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<img src="img/demoDotplot2.png" alt="demoDotplot2" style="border: 1px solid black; width: 400px"></a>
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<tr><td colspan="2">There is very little difference between the <ttp>Dot Plots</ttp>. The
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<tr><td colspan="2">There is very little difference between the <span class="ttp">Dot Plots</span>. The
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difference in the synteny algorithm are obvious on the more complicated examples, as shown in
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<a href="SystemHelp.html#synResults" target="_blank" class="ext">Synteny Results</a>.
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</table>
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<!----------------------------------------------------------->
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<!-- ============================================ -->
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<p>
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<a id="draft"></a> <!-- ref -->
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<h3>Draft: Demo-Draft to Demo-Seq2</h3>
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<table style="width: 800px;">
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<tr><td colspan="2">The <tt>Demo-draft</tt> was run against
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the <tt>Demo-Seq2</tt> with its <ttx>order_against</ttx> parameter set to <tt>Demo_Seq2</tt>;
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<tr><td colspan="2">The <span class="ttt">Demo-draft</span> was run against
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the <span class="ttt">Demo-Seq2</span> with its <span class="ttx">order_against</span> parameter set to <span class="ttt">Demo_Seq2</span>;
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this is explained in detail in the <a href="SystemGuide.html#draft" target="_blank" class="ext">System Guide</a>.
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The resulting dot plot is shown on the right. Note that the 43 contigs
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are ordered, but still fragmented.
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<p>
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<tr><td style="vertical-align: text-top;">
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<a href="img/demoSumDraft.png">
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<a href="img/demoSumDraft.png">
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<img src="img/demoSumDraft.png" alt="demoSumDraft" style="border: 1px solid black; width: 340px"></a>
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<td><a href="img/demoDraft2.png">
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<td><a href="img/demoDraft2.png">
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<img src="img/demoDraft2.png" alt="demoDraft2" style="border: 1px solid black; width: 400px"></a>
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<tr><td>&nbsp;
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<tr><td colspan=2>When the ordering algorithm is run, it creates a new project called <tt>Demo-Draft.Demo_Seq2</tt>,
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<tr><td>&nbsp;<td>&nbsp;
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<tr><td colspan=2>When the ordering algorithm is run, it creates a new project called
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<span class="ttt">Demo-Draft.Demo_Seq2</span>,
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where the 43 contigs are written into three chromosomes; the first two correspond
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to chr1 and chr3 of <tt>Demo_Seq2</tt>, and chr0 contains the contigs that do not align.
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<p>The new project <tt>Demo-Draft.Demo_Seq2</tt>
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was aligned with <tt>Demo_Seq2</tt>, resulting in the dot plot shown on the right.
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to chr1 and chr3 of <span class="ttt">Demo_Seq2</span>, and chr0 contains the contigs that do not align.
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<p>The new project <span class="ttt">Demo-Draft.Demo_Seq2</span>
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was aligned with <span class="ttt">Demo_Seq2</span>, resulting in the dot plot shown on the right.
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<tr><td style="vertical-align: text-top;">
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<a href="img/demoSumOrd.png">
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<a href="img/demoSumOrd.png">
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<img src="img/demoSumOrd.png" alt="demoSumOrd" style="border: 1px solid black; width: 340px"></a>
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<td><a href="img/demoDraftOrd.png">
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<td><a href="img/demoDraftOrd.png">
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<img src="img/demoDraftOrd.png" alt="demoDraftOrd" style="border: 1px solid black; width: 400px"></a>
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</table>
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<!-------------------------------------------------------------------->
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<!----------------------------------------------------------->
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<!-- ===================================================== -->
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<a id="self"></a> <!-- ref -->
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<h3>Self-synteny: Demo-Seq</h3>
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<table class="tx">
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<tr><td colspan="2"><tt>Demo-Seq</tt> has been run against itself.
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<tr><td colspan="2"><span class="ttt">Demo-Seq</span> has been run against itself.
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There are a few blocks, but these blocks are probably too small to be meaningful.
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The blocks below the diagonal are mirrored above
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the diagonal, e.g. 3.5.1 and 5.3.1 are the same.
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<td><a href="img/demoSelf.png">
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<img src="img/demoSelf.png" alt="demoSelf" style="border: 1px solid black; width: 400px"></a>
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</table>
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<!-------------------------------------------------------------------->
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<!---slog ref'ed----------------------------------------------------------------->
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<!-- ============================================================ -->
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<!---slog ref'ed -->
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<a id="slog"></a>
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<h2>symap.log</h2>
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The following 4 sections show the contents of the <ttx>logs/&lt;proj-to-proj&gt;/symap.log</ttx> file:
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The following 4 sections show the contents of the <span class="ttx">logs/&lt;proj-to-proj&gt;/symap.log</span> file:
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<table class="tz"><tr>
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<td><a href="#algo1off">Algo1 !verbose</a>
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<td><a href="#algo1on">Algo1 verbose</a>
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Cluster Algo1 (modified original) or Cluster Algo2 (exon-intron)
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Synteny Strict
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</pre>
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The 2 MUMmer files indicates the chromosome were not split and <ttx>Concat</ttx> was
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The 2 MUMmer files indicates the chromosome were not split and <span class="ttx">Concat</span> was
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used. These two facts along with the number of CPUs can make subtle differences in
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the output.
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<p>
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<!-------------------------------------------------------------------->
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<!-- ========================================================== -->
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<a id="algo1off"></a>
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<b>Algo1 !verbose</b>
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Finish Synteny 2s
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</small></pre>
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<!-------------------------------------------------------------------->
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<!-- ============================================================== -->
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<a id="algo1on"></a>
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<b>Algo1 verbose</b>
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10 Collinear Sets not in blocks (20 total hits)
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Finish Synteny 2s
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</small></pre>
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<!-------------------------------------------------------------------->
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<a id="algo2off"></a>
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<b>Algo2 !verbose</b>
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<pre><small>
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Finish Synteny 1s
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</small></pre>
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<!-------------------------------------------------------------------->
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<b>Algo2 verbose</b>
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<table style="width: 95%"><tr><td style="text-align: left">
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<td style="text-align: right"><a href="#top">Go to top</a></td></tr></table>
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<!---- END BODY -->
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<!-- END BODY -->
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<p class="trailer"> Email Comments To: <a href="mailto:cas1@arizona.edu">cas1@arizona.edu</a></p>
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</div>
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