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  <TITLE> EMBOSS: gsvalue </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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gsvalue
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<H2> Function </H2>
   Calculate the strength of selected codon usage bias (S)
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<H2>Description</H2>
<p>
   gsvalue calculates the strength of selected codon usage bias (S), also<br />
   known as Sharp's S index. Using four codon pairs that are recognized by the<br />
   same tRNA anticodon, namely, Phe(UUC and UUU), Ile(AUC and AUU), Tyr(UAC and<br />
   UAU), and Asn(AAC and AAU), since the former in each of the pairs has<br />
   stronger Watson-Crick pairing, selection towards the former codon can be<br />
   observed for highly expressed genes. S index is therefore the weighted<br />
   average of such bias, giving an over-all value for a genome, indicating its<br />
   strength of selected codon usage bias. See Sharp et al. (2005) for details.<br />
   Sharp originally defined 40 genes as the highly expressed gene group, with<br />
   tufA, tsf, fusA, rplA-rplF, rplI-rplT, rpsB-rpsT. Since the identificaiton<br />
   of these genes is not convenient for computational automation, by default,<br />
   this method uses ribosomal proteins as the highly expressed gene group,<br />
   as used by Viera-silva and Rocha (2010).<br />
   However, Sharp's gene group can be optionally used with -sharp option.<br />
   With this option, all of the 40 genes must be named accordingly in the given<br />
   genome file.<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>

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

Here is a sample session with gsvalue

% gsvalue refseqn:NC_000913
Calculate the strength of selected codon usage bias (S)
Codon usage output file [nc_000913.gsvalue]: 

</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>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>Codon usage output file</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.gsvalue</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>-sharp</td>
<td>boolean</td>
<td>Include to use the 40 genes used by Sharp instead of ribosomal proteins</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>

</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 />
   gsvalue reads one or more nucleotide sequences.<br />
<br />

</p>

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

<p>
   The output from gsvalue is to a plain text file.<br />
<br />
   File: nc_000913.gsvalue<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913 S-value: 1.23467100598485<br />
</td></tr></table>

</p>

<h2>Data files</h2>

<p>
None.
</p>

<h2>Notes</h2>

<p>
None.
</p>

<h2>References</h2>

<pre>
   Sharp PM et al. (2005) "Variation in the strength of selected codon usage
      bias among bacteria", Nucleic Acids Research, 33(4):1141-1153

   Vieira-Silva S and Rocha EPC (2010) "The systemic imprint of growth and its
      uses in ecological (meta)genomics", PLoS Genetics, 6(1):e1000808

   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="gcbi.html">gcbi</a></td>
<td>Calculates the codon bias index (CBI)</td>
</tr><tr>
<td><a href="gdeltaenc.html">gdeltaenc</a></td>
<td>Calculate the codon usage bias related to translation optimization              (delta ENC)</td>
</tr><tr>
<td><a href="gicdi.html">gicdi</a></td>
<td>Calculates the intrinsic codon deviation index (ICDI)</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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