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      <h1 class="project-name">The DIGS Tool</h1>
      <h2 class="project-tagline">Explore genomes interactively using BLAST and a relational database.</h2>
      
      <a href="../index.html" class="btn">Home</a>
      <a href="https://github.com/giffordlabcvr/DIGS-tool/wiki/Installation-and-Setup" class="btn">User Guide</a>
      <a href="https://github.com/giffordlabcvr/DIGS-tool/zipball/master" class="btn">Download</a>
      <a href="https://github.com/giffordlabcvr/DIGS-tool" class="btn">View on GitHub</a>
      
    </section>

    <section class="main-content">


	   <h3>
		 <a id="howToRunDigs" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>How to run the DIGS tool</strong>
	   </h3>
       <hr>

	   <p>
		  This tutorial assumes that you have installed the DIGS tool and comprises the following steps:

		 <ol>
		   <li> Set up target library.</li>
		   <li> Set up reference library.</li>
		   <li> Set up probe library.</li>
		   <li> Run a screen.</li>
		   <li> Inspecting results.</li>
		   <li> Update reference sequences and reassign.</li>
		   <li> Consolidate.</li>
		 </ol>

 	   </p>
 	   
       <br>
	   <h3>
		 <a id="setUpTargetLibrary" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Set up target library</strong>
	   </h3>
       <hr>

	   <p>
		  The DIGS tool is designed to perform systematic, simialrity-search based screening
		  of local DNA sequence 'databases'.
		  A local DNA sequence 'database' is a collection of FASTA formatted DNA sequences.
		  This is the form that most genome and transcriptome assemblies are distributed. 
 	   </p>


	   <p>
		  The DIGS tool uses the BLAST program suite to perform similarity searches. 
		  BLAST can be used to search any file containing FASTA-formatted sequences for
		  similar sequences. 
 	   </p>

       <br>
	   <h3>
		 <a id="setUpReferenceLibrary" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Set up reference library</strong>
	   </h3>
       <hr>


       <br>
	   <h3>
		 <a id="setUpProbes" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Set up probe library</strong>
	   </h3>
       <hr>


       <br>
	   <h3>
		 <a id="RunScreen" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Run a screen</strong>
	   </h3>
       <hr>


	   <p>
          Run the DIGS tool as follows.
 	   
 
   <pre>
   <code>./digs_tool.pl -m=2 -i input.ctl</code></pre>
   
	   </p>



       <br>
	   <h3>
		 <a id="InspectResults" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Inspecting results</strong>
	   </h3>
       <hr>


       <br>
	   <h3>
		 <a id="UpdateRefSeqsAndReassign" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Update reference sequences and reassign</strong>
	   </h3>
       <hr>





	 <footer class="site-footer">
	   <span class="site-footer-owner"><a href="https://github.com/giffordlabcvr/DIGS-tool">DIGS for EVEs</a> is maintained by <a href="https://github.com/giffordlabcvr">giffordlabcvr</a>.</span>

	   <span class="site-footer-credits">This page was generated by <a href="https://pages.github.com">GitHub Pages</a> using the <a href="https://github.com/jasonlong/cayman-theme">Cayman theme</a> by <a href="https://twitter.com/jasonlong"><NAME></a>.</span>
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</html><commit_msg>Updated content<commit_after><!DOCTYPE html>
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    <title>How to run the DIGS tool</title>
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  </head>
  
  <body>
    <section class="page-header">
    
      <h1 class="project-name">The DIGS Tool</h1>
      <h2 class="project-tagline">Explore genomes interactively using BLAST and a relational database.</h2>
      
      <a href="../index.html" class="btn">Home</a>
      <a href="https://github.com/giffordlabcvr/DIGS-tool/wiki/Installation-and-Setup" class="btn">User Guide</a>
      <a href="https://github.com/giffordlabcvr/DIGS-tool/zipball/master" class="btn">Download</a>
      <a href="https://github.com/giffordlabcvr/DIGS-tool" class="btn">View on GitHub</a>
      
    </section>

    <section class="main-content">


	   <h3>
		 <a id="howToRunDigs" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>How to run the DIGS tool</strong>
	   </h3>
       <hr>

	   <p>
		  This tutorial assumes that you have installed the DIGS tool and comprises the following steps:

		 <ol>
		   <li> Set up target library</li>
		   <li> Set up reference library</li>
		   <li> Set up probe library</li>
		   <li> Set up a control file</li>
		   <li> Run a screen</li>
		   <li> Inspecting results</li>
		   <li> Update reference sequences and reassign</li>
		   <li> Consolidate</li>
		 </ol>

 	   </p>
 	   
       <br>
	   <h3>
		 <a id="setUpTargetLibrary" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Set up target library</strong>
	   </h3>
       <hr>

	   <p>
		  The DIGS tool is designed to perform systematic, simialrity-search based screening
		  of <b>local DNA sequence 'databases'</b> - in other words, collections of FASTA
		  formatted DNA sequences.
		  This is the form that most genome and transcriptome assemblies are distributed. 
 	   </p>


	   <p>
		  The DIGS tool uses the BLAST program suite to perform similarity searches. 
		  BLAST can be used to search any file containing FASTA-formatted sequences for
		  similar sequences. 
 	   </p>


       <br>
	   <h3>
		 <a id="setUpReferenceLibrary" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Set up reference library</strong>
	   </h3>
       <hr>


	   <p>

          DIGS requires a library of FASTA-formatted reference sequences for the gene
          or genetic element under investigation. 
          Probes for screening are selected from the reference library.
          
 	   </p>


	   <p>
	   
          The DIGS tool uses a simple rule to capture data from the headers of
          FASTA-formatted reference (and probe) sequences; headers should be structured
          so as to define two hierarchical name elements; ‘name’ and ‘gene_name’,
          separated by an underscore. In the example shown above these are a virus name
          and a gene name. Other two-level hierarchical naming schemes (e.g. species &
          gene name, gene-subdomain name) can also be used, providing the same scheme is
          used consistently throughout the project. Reference sequences should be stored
          in a file, the path to which will be specified in the DIGS control file.
          
 	   </p>



 

       <br>
	   <h3>
		 <a id="setUpProbes" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Set up probe library</strong>
	   </h3>
       <hr>

	   <p>
	   

          A subset of reference sequences should be selected as probes.
          The entire reference library can be used - in which case there is no need to
          create a separate file – but it is often sufficient to use only a subset of
          sequences from the reference sequence library, in which case, a separate file
          containing this subset should be created.
          The path to this file is specified in the DIGS control file.

 	   </p>



       <br>
	   <h3>
		 <a id="SetUpControlFile" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Set up control file</strong>
	   </h3>
       <hr>



	   <p>
          The DIGS control file contains parameters and paths for DIGS.
          Control files are structured as NEXUS style blocks delineated by BEGIN and
          ENDBLOCK tokens.
          An annotated example of a DIGS control file is shown below.
          Note that not all parameters will need to be defined for every screen.

 	   </p>

       <br>
	   <h3>
		 <a id="RunScreen" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Run a screen</strong>
	   </h3>
       <hr>


	   <p>
          Run the DIGS tool as follows.
 	   
 
   <pre>
   <code>./digs_tool.pl -m=2 -i input.ctl</code></pre>
   
	   </p>



       <br>
	   <h3>
		 <a id="InspectResults" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Inspecting results</strong>
	   </h3>
       <hr>


	   <p>
	   

          A MySQL client like SequelPro

 	   </p>


       <br>
	   <h3>
		 <a id="UpdateRefSeqsAndReassign" class="anchor" href="#sequenceData" aria-hidden="true"><span aria-hidden="true" class="octicon octicon-link"></span></a><strong>Update reference sequences and reassign</strong>
	   </h3>
       <hr>





	 <footer class="site-footer">
	   <span class="site-footer-owner"><a href="https://github.com/giffordlabcvr/DIGS-tool">DIGS for EVEs</a> is maintained by <a href="https://github.com/giffordlabcvr">giffordlabcvr</a>.</span>

	   <span class="site-footer-credits">This page was generated by <a href="https://pages.github.com">GitHub Pages</a> using the <a href="https://github.com/jasonlong/cayman-theme">Cayman theme</a> by <a href="https://twitter.com/jasonlong"><NAME></a>.</span>
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