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  <TITLE> EMBOSS: gcodoncompiler </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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<b><font size="+6">
gcodoncompiler
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<br>&nbsp;
<p>


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<H2> Function </H2>
   Calculate various kinds of amino acid and codon usage data
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<H2>Description</H2>
<p>
   gcodoncompiler calculates various kinds of amino acid and codon usage data.<br />
   The following values are calculable:<br />
      A0: Absolute amino acid frequency<br />
      A1: Relative amino acid frequency<br />
      C0: Absolute codon frequency<br />
      C1: Relative codon frequency in a complete sequence<br />
      C2: Relative codon frequency in each amino acid<br />
      C3: Relative synonymous codon usage<br />
      C4: Relative adaptiveness<br />
      C5: Maximum or minor codon<br />
   For amino acids unpresent in a gene, C2-C3 does not calculate the values.<br />
   By using R* in place, such values are hypothesized that alternative<br />
   synonymous codons are used with equal frequency.<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 gcodoncompiler

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

% gcodoncompiler refseqn:NC_000913
Calculate various kinds of amino acid and codon usage data
Codon usage output file [nc_000913.gcodoncompiler]: 

</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>.gcodoncompiler</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 to translate using standard codon table</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-startcodon</td>
<td>boolean</td>
<td>Include to include start codon</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-stopcodon</td>
<td>boolean</td>
<td>Include to include stop codon</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 (i.e. amino acids and nucleotides)</td>
<td>Any string</td>
<td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-data</td>
<td>list</td>
<td>Kinds of codon usage data. R* hypothesizes amino acids which are not present in the gene</td>
<td><table><tr><td>A0</td> <td><i>(Absolute amino acid frequency ('AA'))</i></td></tr><tr><td>A1</td> <td><i>(Relative amino acid frequency ('RAAU'))</i></td></tr><tr><td>C0</td> <td><i>(Absolute codon frequency ('AF'))</i></td></tr><tr><td>C1</td> <td><i>(Relative codon frequency in a complete sequence)</i></td></tr><tr><td>C2</td> <td><i>(Relative codon frequency in each amino acid ('RF'))</i></td></tr><tr><td>C3</td> <td><i>(Relative synonymous codon usage ('RSCU'))</i></td></tr><tr><td>C4</td> <td><i>(Relative adaptiveness)</i></td></tr><tr><td>i.e., ratio to maximum of minor codon ('W') C5</td> <td><i>(Maximum (1) or minor (0) codon)</i></td></tr><tr><td>R0</td> <td><i>(Absolute codon frequency ('AF'))</i></td></tr><tr><td>R1</td> <td><i>(Relative codon frequency in a complete sequence)</i></td></tr><tr><td>R2</td> <td><i>(Relative codon frequency in each amino acid ('RF'))</i></td></tr><tr><td>R3</td> <td><i>(Relative synonymous codon usage ('RSCU'))</i></td></tr><tr><td>R4</td> <td><i>(Relative adaptiveness)</i></td></tr><tr><td>i.e., ratio to maximum of minor codon ('W') R5</td> <td><i>(Maximum (1) or minor (0) codon)</i></td></tr></table></td>
<td>R0</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 />
   gcodoncompiler reads one or more nucleotide sequences.<br />
<br />

</p>

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

<p>
   The output from gcodoncompiler is to a plain text file.<br />
<br />
   File: nc_000913.gcodoncompiler<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
Agca,Agcc,Agcg,Agct,Ctgc,Ctgt,Dgac,Dgat,Egaa,Egag,Fttc,Fttt,Ggga,Gggc,Gggg,Gggt,Hcac,Hcat,Iata,Iatc,Iatt,Kaaa,Kaag,Lcta,Lctc,Lctg,Lctt,Ltta,Lttg,Matg,Naac,Naat,Pcca,Pccc,Pccg,Pcct,Qcaa,Qcag,Raga,Ragg,Rcga,Rcgc,Rcgg,Rcgt,Sagc,Sagt,Stca,Stcc,Stcg,Stct,Taca,Tacc,Tacg,Tact,Utga,Vgta,Vgtc,Vgtg,Vgtt,Wtgg,Ytac,Ytat,locus_tag<br />
26551,33911,44924,20010,8486,6707,25234,42161,52362,23474,21841,29334,10226,39395,14472,32678,12830,16952,5356,33359,40221,44272,13398,5079,14709,70441,14410,18097,17936,32971,28329,22786,11063,7142,30994,9130,20216,38169,2495,1366,4529,29308,6991,27864,21132,11323,9159,11332,11759,10992,8979,31001,18989,11581,3,14337,20240,34499,24056,20071,16088,21069,<br />
</td></tr></table>

</p>

<h2>Data files</h2>

<p>
None.
</p>

<h2>Notes</h2>

<p>
None.
</p>

<h2>References</h2>

<pre>
   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="gaminoinfo.html">gaminoinfo</a></td>
<td>Prints out basic amino acid sequence statistics</td>
</tr><tr>
<td><a href="gaaui.html">gaaui</a></td>
<td>Calculates various indece of amino acid usage</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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