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  <TITLE> EMBOSS: gbaseentropy </TITLE>
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<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<A HREF="/" ONMOUSEOVER="self.status='Go to the EMBOSS home page';return true"><img border=0 src="http://soap.g-language.org/gembassy/emboss_explorer/manual/emboss_icon.jpg" alt="" width=150 height=48></a>
</td>
<td align=left valign=middle>
<b><font size="+6">
gbaseentropy
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<!--END OF HEADER-->






<H2> Function </H2>
   Calculates and graphs the sequence conservation using Shanon uncertainty (entropy)
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
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<H2>Description</H2>
<p>
   This function calculates and graphs the sequence conservation in regions<br />
   around the start/stop codons using Shanon uncertainty (entropy). Smaller<br />
   values resemble higher conservation where the minumum value is 0 and the<br />
   maximum value is 2. The entropy is typically the lowest around position 0<br />
   (start/stop codon position).<br />
    <br />
   G-language SOAP service is provided by the<br />
   Institute for Advanced Biosciences, Keio University.<br />
   The original web service is located at the following URL:<br />
<br />
   http://www.g-language.org/wiki/soap<br />
<br />
   WSDL(RPC/Encoded) file is located at:<br />
<br />
   http://soap.g-language.org/g-language.wsdl<br />
<br />
   Documentation on G-language Genome Analysis Environment methods are<br />
   provided at the Document Center<br />
<br />
   http://ws.g-language.org/gdoc/<br />
<br />

</p>

<H2>Usage</H2>

Here is a sample session with gbaseentropy

<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% gbaseentropy refseqn:NC_000913
Calculates and graphs the sequence conservation using Shanon uncertainty
(entropy)
Program compseq output file (optional) [nc_000913.gbaseentropy]: 

</pre></td></tr></table>

Go to the <a href="#input">input files</a> for this example<br>
Go to the <a href="#output">output files</a> for this example<br><br>

   Example 2

<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% gbaseentropy refseqn:NC_000913 -plot -graph png
Calculates and graphs the sequence conservation using Shanon uncertainty
(entropy)
Created gbaseentropy.1.png

</pre></td></tr></table>

Go to the <a href="#input">input files</a> for this example<br>
Go to the <a href="#output">output files</a> for this example<br><br>

<h2>Command line arguments</h2>

<table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
<tr bgcolor="#FFFFCC">
<th align="left">Qualifier</th>
<th align="left">Type</th>
<th align="left">Description</th>
<th align="left">Allowed values</th>
<th align="left">Default</th>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-sequence]<br>(Parameter 1)</td>
<td>seqall</td>
<td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
<td>Readable sequence(s)</td>
<td><b>Required</b></td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-graph</td>
<td>xygraph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-outfile</td>
<td>outfile</td>
<td>Program compseq output file (optional)</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.gbaseentropy</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>

<tr>
<td colspan=5>(none)</td>
</tr>

<tr bgcolor="#FFFFCC">
<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
</tr>

<tr bgcolor="#FFFFCC">
<td>-position</td>
<td>selection</td>
<td>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</td>
<td>Choose from selection list of values</td>
<td>start</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-patlen</td>
<td>integer</td>
<td>Length of oligomer to count</td>
<td>Any integer value</td>
<td>3</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-upstream</td>
<td>integer</td>
<td>Length upstream of specified position to create PWM</td>
<td>Any integer value</td>
<td>30</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-downstream</td>
<td>integer</td>
<td>Length downstream of specified position to create PWM</td>
<td>Any integer value</td>
<td>30</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-[no]accid</td>
<td>boolean</td>
<td>Include to use sequence accession ID as query</td>
<td>Boolean value Yes/No</td>
<td>Yes</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-plot</td>
<td>toggle</td>
<td>Include to plot result</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>

</table>


<h2 id="input">Input file format</h2>

<p>
   The database definitions for following commands are available at<br />
   http://soap.g-language.org/kbws/embossrc<br />
<br />
   gbaseentropy reads one or more nucleotide sequences.<br />
<br />

</p>

<h2 id="output">Output file format</h2>

<p>
   The output from gbaseentropy is to a plain text file or the EMBOSS graphics device.<br />
<br />
   File: nc_000913.gbaseentropy<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
-30,1.98284<br />
-29,1.97873<br />
-28,1.97692<br />
-27,1.97595<br />
-26,1.97094<br />
-25,1.96777<br />
-24,1.96272<br />
-23,1.96288<br />
-22,1.95707<br />
<br />
<font color=red>[Part of this file has been deleted for brevity]</font><br />
<br />
21,1.93528<br />
22,1.94470<br />
23,1.95204<br />
25,1.93139<br />
25,1.95640<br />
26,1.95711<br />
27,1.93785<br />
28,1.96060<br />
29,1.94316<br />
30,1.92581<br />
</td></tr></table>

</p>

<h3>Data files</h2>

<p>
None.
</p>

<h2>Notes</h2>

<p>
None.
</p>

<h2>References</h2>

<pre>
   Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
      Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
      for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.

   Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
      large-scale analysis of high-throughput omics data, J. Pest Sci.,
      31, 7.

   Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
      Analysis Environment with REST and SOAP Web Service Interfaces,
      Nucleic Acids Res., 38, W700-W705.

</pre>

<h2>Warnings</h2>

<p>
None.
</p>

<h2>Diagnostic Error Messages</h2>

<p>
None.
</p>

<h2>Exit status</h2>

<p>
It always exits with a status of 0.
</p>

<h2>Known bugs</h2>

<p>
None.
</p>

<h2>See also</h2>

<table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
<th>Description</th></tr>

<tr>
<td><a href="gbaseinformationcontent.html">gbaseinformationcontent</a></td>
<td>Calculates and graphs the sequence conservation using information content</td>
</tr>
<tr>
<td><a href="gbaserelativeentropy.html">gbaserelativeentropy</a></td>
<td>Calculates and graphs the sequence conservation using Kullback-Leibler divergence (relative entropy)</td>
</tr>
</table>

<h2>Author(s)</h2>

<pre>
Hidetoshi Itaya (celery@g-language.org)
  Institute for Advanced Biosciences, Keio University
  252-0882 Japan

Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
  Institute for Advanced Biosciences, Keio University
  252-0882 Japan</pre>

<h2>History</h2>

   2012 - Written by Hidetoshi Itaya

<h2>Target users</h2>

   This program is intended to be used by everyone and everything, from
   naive users to embedded scrips.

<h2>Comments</h2>

   None.

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