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  <TITLE> EMBOSS: ggenomicskew </TITLE>
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<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>
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<b><font size="+6">
ggenomicskew
</font></b>
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<br>&nbsp;
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<H2> Function </H2>
   Calculates the GC skew in different regions of the given genome
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<H2>Description</H2>
<p>
   ggenomicskew calculates and plots the GC skew for the whole genome, coding<br />
   regions, intergenic regions, and the third codon. This program is useful in<br />
   visualizing various base composition bias within the genome. AT skew can be<br />
   calculated instead of GC skew by toggling the -at qualifier.<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 ggenomicskew

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

% ggenomicskew refseqn:NC_000913
Calculates the GC skew in different regions of the given genome
Program compseq output file (optional) [nc_000913.ggenomicskew]: 

</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>

% ggenomicskew refseqn:NC_000913 -plot -graph png
Calculates the GC skew in different regions of the given genome
Created ggenomicskew.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>.ggenomicskew</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>-divide</td>
<td>integer</td>
<td>Window to divide into</td>
<td>Any integer value</td>
<td>250</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-at</td>
<td>boolean</td>
<td>Input 1 when observing AT skew instead of GC skew</td>
<td>Boolean value Yes/No</td>
<td>No</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 />
   ggenomicskew reads one or more nucleotide sequences.<br />
<br />

</p>

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

<p>
   The output from ggenomicskew is to a plain text file or the EMBOSS graphics device.<br />
<br />
   File: nc_000913.ggenomicskew<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
location,GC skew,coding,intergenic,third codon<br />
0,-0.036259,-0.040085,-0.034707,-0.141888,<br />
1,-0.031167,-0.035657,0.047953,-0.175758,<br />
2,-0.028670,-0.031139,-0.049143,-0.018466,<br />
3,-0.016647,-0.004656,-0.102616,0.086181,<br />
4,-0.041985,-0.029846,-0.088670,0.015291,<br />
5,-0.097093,-0.103813,-0.067275,-0.247401,<br />
6,-0.028028,-0.016363,-0.048806,-0.047332,<br />
7,-0.055805,-0.059329,-0.020071,-0.123271,<br />
<br />
<font color=red>[Part of this file has been deleted for brevity]</font><br />
<br />
241,0.000772,-0.012151,-0.063786,0.069585,<br />
242,-0.025787,-0.000384,-0.049143,0.029431,<br />
243,0.010516,0.008217,-0.030600,0.128657,<br />
244,-0.037115,-0.015134,0.017500,0.035398,<br />
245,-0.000317,0.006021,-0.047170,0.091549,<br />
246,-0.025417,-0.015190,-0.116608,0.044619,<br />
247,-0.038404,-0.035676,-0.135714,0.015375,<br />
248,-0.026246,-0.024240,-0.037190,-0.130118,<br />
249,-0.053371,-0.057225,-0.022472,-0.082167,<br />
250,-0.026316,0.166667,-0.151515,0.000000,<br />
</td></tr></table>

</p>

<h2>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="ggcskew.html">ggcskew</a></td>
<td>Calculates the GC skew of the input sequence</td>
</tr><tr>
<td><a href="ggcwin.html">ggcwin</a></td>
<td>Calculates the GC content along the given genome</td>
</tr><tr>
<td><a href="ggeneskew.html">ggeneskew</a></td>
<td>Calculate the gene strand bias of the given genome</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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