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<!--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> <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><*></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>