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  <TITLE> EMBOSS: gfop </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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gfop
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<H2> Function </H2>
   Calculate the frequency of optimal codons (Fop)
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<H2>Description</H2>
<p>
   gfop calculates the frequency of optimal codons (Fop).Fop is an index to
<br />
   show the optimization level of synonymous codon usage choice. It is<br />
   basically a ratio of optimal codons against all codons used. The value<br />
   of Fop ranges from 0 (no optimal codons are used) and 1 (only optimal<br />
   codons are used).<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 gfop

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

% gfop refseqn:NC_000913
Calculate the frequency of optimal codons (Fop)
Codon usage output file [nc_000913.gfop]: 

</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>.gfop</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>-translate</td>
<td>boolean</td>
<td>Include when translates using standard codon table</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 />
   gfop reads one or more nucleotide sequences.<br />
<br />

</p>

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

<p>
   The output from gfop is to a plain text file.<br />
<br />
   File: nc_000913.gfop<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
Laa,Lc,fop,gene<br />
20,5,0.4000,thrL<br />
819,133,0.4361,thrA<br />
309,46,0.4783,thrB<br />
427,69,0.5217,thrC<br />
97,7,0.2857,yaaX<br />
257,56,0.4643,yaaA<br />
475,96,0.3958,yaaJ<br />
316,56,0.6964,talB<br />
<br />
<font color=red>[Part of this file has been deleted for brevity]</font><br />
<br />
169,27,0.2593,yjjX<br />
214,23,0.5652,ytjC<br />
288,49,0.4082,rob<br />
156,23,0.3478,creA<br />
228,26,0.3462,creB<br />
473,69,0.3478,creC<br />
449,70,0.3286,creD<br />
237,46,0.6957,arcA<br />
45,10,0.7000,yjjY<br />
227,24,0.2500,yjtD<br />
</td></tr></table>

</p>

<h2>Data files</h2>

<p>
None.
</p>

<h2>Notes</h2>

<p>
None.
</p>

<h2>References</h2>

<pre>
   Ikemura, T. (1981) Correlation between the abundance of Escherichia coli
      transfer RNAs and the occurrence of the respective codons in its protein
      genes: a proposal for a synonymous codon choice that is optimal for the
      E. coli translational system, J.Mol.Biol, 151:389-409.

   Ikemura (1985) Codon usage and tRNA content in unicellular and multicellular
      organisms, Mol.Biol.Evol, 2(1):13-34.

   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="gscs.html">gscs</a></td>
<td>Calculates the scaled chi-square</td>
</tr><tr>
<td><a href="gwvalue.html">gwvalue</a></td>
<td>Calculate the 'relative adaptiveness of each codon' (W)</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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