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  <TITLE> EMBOSS: gphx </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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gphx
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<br>&nbsp;
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<H2> Function </H2>
   Identify predicted highly expressed gene
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<H2>Description</H2>
<p>
   gphx calculates codon usage differences between gene classes for identifying<br />
   Predicted Highly eXpressed (PHX) and Putative Alien (PA) genes. A gene is<br />
   identified as PHX if BgC/BgH >= 1, where BgC and BgH is a value < 1 by it's<br />
   nature. PHX genes are known to generally have favorable codon usage, strong<br />
   SD sequences, and probably stronger conservation of promoter sequences.<br />
   A gene is idenfitied as PA if BgC and BgH is greater than the median of<br />
   BgC for every gene with a length close to the gene.<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 gphx

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

% gphx refseqn:NC_000913
Identify predicted highly expressed gene
Codon usage output file [nc_000913.gphx]: 

</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>.gphx</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 translating using standard codon table</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-delkey</td>
<td>string</td>
<td>Regular expression to delete key</td>
<td>Any string</td>
<td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</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 />
   gphx reads one or more nucleotide sequences.<br />
<br />

</p>

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

<p>
   The output from gphx is to a plain text file.<br />
<br />
   File: nc_000913.gphx<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
BgC,BgH,E_g,phx,pa,gene<br />
0.8070,0.8977,0.8990,0,1,thrL<br />
0.1857,0.5958,0.3116,0,0,thrA<br />
0.2323,0.5964,0.3896,0,0,thrB<br />
0.2353,0.6064,0.3881,0,0,thrC<br />
0.4353,0.6020,0.7231,0,1,yaaX<br />
0.2961,0.6790,0.4361,0,0,yaaA<br />
0.2233,0.7009,0.3186,0,0,yaaJ<br />
0.4149,0.3071,1.3511,1,0,talB<br />
<br />
   [Part of this file has been deleted for brevity]<br />
<br />
0.3255,0.7038,0.4625,0,0,yjjX<br />
0.3531,0.5906,0.5979,0,0,ytjC<br />
0.2257,0.5235,0.4311,0,0,rob<br />
0.3584,0.6809,0.5264,0,0,creA<br />
0.3455,0.7950,0.4346,0,0,creB<br />
0.2298,0.7154,0.3212,0,0,creC<br />
0.3299,0.7916,0.4167,0,0,creD<br />
0.3543,0.3786,0.9357,0,0,arcA<br />
0.7295,0.8286,0.8804,0,1,yjjY<br />
0.4028,0.8401,0.4795,0,0,yjtD<br />
</td></tr></table>

</p>

<h2>Data files</h2>

<p>
None.
</p>

<h2>Notes</h2>

<p>
None.
</p>

<h2>References</h2>

<pre>
   CMBL- PHX/PA user guide http://www.cmbl.uga.edu/software/PHX-PA-guide.htm

   Henry I., Sharp PM. (2007) Predicting gene expression level from codon
      usage bias Mol Biol Evol, 24(1):10-2.

   Karlin S., and Mrazek J. (2000) Predicted highly expressed genes of diverse
      prokaryotic genomes J.Bacteriol, 182(18):5238-5250.

   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="gcai.html">gcai</a></td>
<td>Calculate codon adaptation index for each gene</td>
</tr><tr>
<td><a href="gp2.html">gp2</a></td>
<td>Calculate the P2 index of each gene</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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