Mercurial > repos > ktnyt > gembassy

<!--START OF HEADER - DON'T ALTER -->

<HTML>
<HEAD>
  <TITLE> EMBOSS: gp2 </TITLE>
</HEAD>
<BODY BGCOLOR="#FFFFFF" text="#000000">


<table align=center border=0 cellspacing=0 cellpadding=0>
<tr><td valign=top>
<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>
</td>
<td align=left valign=middle>
<b><font size="+6">
gp2
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<!--END OF HEADER-->


<H2> Function </H2>
   Calculate the P2 index of each gene
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->


<H2>Description</H2>
<p>
   gp2 calculates the P2 index for each gene. This index describes<br />
   the proportion of codons conforming to the intermediate strength of<br />
   codon-anticodon interaction energy rule of Grosjean and Fiers:<br />
   P2 = (WWC+SSU)/(WWY+SSY) where W = A or U, S = C or G, and Y = C or U.<br />
   It indicates the efficiency of the codon-anticodon interaction, and has<br />
   been used as an indicator of the presence of translational selection.<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 gp2

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

% gp2 refseqn:NC_000913
Calculate the P2 index of each gene
Codon usage output file [nc_000913.gp2]:

</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>.gp2</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>-[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 />
   gp2 reads one or more nucleotide sequences.<br />
<br />

</p>

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

<p>
   The output from gp2 is to a plain text file.<br />
<br />
   File: nc_000913.gp2<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
P2,gene<br />
0.4444,thrL<br />
0.4234,thrA<br />
0.4565,thrB<br />
0.5156,thrC<br />
0.4074,yaaX<br />
0.4494,yaaA<br />
0.3621,yaaJ<br />
0.6832,talB<br />
<br />
<font color=red>[Part of this file has been deleted for brevity]</font><br />
<br />
0.3692,yjjX<br />
0.4912,ytjC<br />
0.4271,rob<br />
0.4318,creA<br />
0.3065,creB<br />
0.3851,creC<br />
0.4320,creD<br />
0.6395,arcA<br />
0.7857,yjjY<br />
0.3333,yjtD<br />
</td></tr></table>

</p>

<h2>Data files</h2>

<p>
None.
</p>

<h2>Notes</h2>

<p>
None.
</p>

<h2>References</h2>

<pre>
   Gouy M, Gautier C. (1982) Codon usage in bacteria: correlation with gene
      expressivity, Nucleic Acids Res, 10(22):7055-74.

   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="gphx.html">gphx</a></td>
<td>Identify predicted highly expressed 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.

</BODY>
</HTML>
author	ktnyt
date	Fri, 26 Jun 2015 05:19:29 -0400
parents
children