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  <TITLE> EMBOSS: gwvalue </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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gwvalue
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<br>&nbsp;
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<H2> Function </H2>
   Calculate the 'relative adaptiveness of each codon' (W)
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<H2>Description</H2>
<p>
   gwvalue calculates the 'relative adaptiveness of each codon' (W value)<br />
   which is essential in CAI analysis. W value is calculated by setting the<br />
   best codon to 1 and calculating the proportion of the other codons.<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 gwvalue

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

% gwvalue refseqn:NC_000913
Calculate the 'relative adaptiveness of each codon' (W)
Codon usage output file [nc_000913.gwvalue]: 

</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>.gwvalue</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>-include</td>
<td>string</td>
<td>Regular expression to include genes in a reference set a reference set in several studies are in-built 1: Nakamura and Tabata, 2: Sharp and Li, 3: Sakai et al.</td>
<td>Any string</td>
<td>ribosomal.*protein</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-exclude</td>
<td>string</td>
<td>Regular expression to exclude genes from a reference set</td>
<td>Any string</td>
<td>[Mm]itochondrial</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>Input file format</h2>

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

</p>

<h2>Output file format</h2>

<p>
   The output from gwvalue is to a plain text file.<br />
<br />
   File: nc_000913.gwvalue<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
Reference set of highly expressed genes<br />
product<br />
30S ribosomal subunit protein S20<br />
30S ribosomal subunit protein S2<br />
ribosomal protein S12 methylthiotransferase; radical SAM superfamily<br />
ribosomal protein S6 modification protein<br />
30S ribosomal subunit protein S1<br />
ribosomal-protein-S5-alanine N-acetyltransferase<br />
50S ribosomal subunit protein L32<br />
<br />
<font color=red>[Part of this file has been deleted for brevity]</font><br />
<br />
T,acc,1.0000<br />
T,acg,0.2234<br />
T,act,0.9734<br />
V,gta,0.4960<br />
V,gtc,0.2281<br />
V,gtg,0.3422<br />
V,gtt,1.0000<br />
W,tgg,1.0000<br />
Y,tac,1.0000<br />
Y,tat,0.5310<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 Res. 33(4):1141-1153

   Sakai et al. (2001) Correlation between Shine--Dalgarno sequence
      conservation and codon usage of bacterial genes, J.Mol.Evol. 52:164-170.

   Nakamura and Tabata (1997) Codon-anticodon assignment and detection of
      codon usage trends in seven microbial genomes, Microb.Comp.Genomics
      2:299-312.

   Sharp and Li (1987) The codon Adaptation Index--a measure of directional
      synonymous codon usage bias, and its potential applications, Nucleic
      Acids Res. 15:1281-1295.

   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="genc.html">genc</a></td>
<td>Calculate the effective number of codons (Nc)</td>
</tr><tr>
<td><a href="gew.html">gew</a></td>
<td>Calculate a measure of synonymous codon usage evenness (Ew)</td>
</tr><tr>
<td><a href="gfop.html">gfop</a></td>
<td>Calculate the frequency of optimal codons (Fop)</td>
</tr><tr>
<td><a href="gscs.html">gscs</a></td>
<td>Calculates the scaled chi-square</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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