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date Fri, 26 Jun 2015 05:21:44 -0400
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--- a/GEMBASSY-1.0.3/doc/html/gaaui.html	Fri Jun 26 05:20:29 2015 -0400
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<HTML>
<HEAD>
  <TITLE> EMBOSS: gaaui </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">
gaaui
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<!--END OF HEADER-->






<H2> Function </H2>
   Calculates various indece of amino acid usage
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>Description</H2>
<p>
   gaaui calculates amino acid usage indices for proteins (excluding<br />
   formylmethionine). Calculated indices are as follows,<br />
      Laa:   Length in amino acids<br />
      ndaa:  Number of different amino acids<br />
      Haau:  Entropy of amino acid usage<br />
      mmw:   Mean molecular weight<br />
      gravy: Mean hydropathic indices of each amino acid<br />
      aroma: Relative frequency of aromatic amino acids<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 gaaui

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

% gaaui refseqn:NC_000913
Calculates various indece of amino acid usage
AAINDEX entry output file [nc_000913.gaaui]: 

</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>AAINDEX entry output file</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.gaaui</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 />
   gaaui reads one or more nucleotide sequences.<br />
<br />

</p>

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

<p>
   The output from gaaui is to a plain text file.<br />
<br />
   File: nc_000913.gaaui<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
Laa,ndaa,Haau,mmw,gravy,aroma,gene<br />
20,8,2.4842,117.48,+0.0150,0.0000,thrL<br />
819,20,4.0887,126.65,+0.0328,0.0659,thrA<br />
309,20,4.1228,126.35,+0.0181,0.0712,thrB<br />
427,20,4.0806,128.00,-0.1014,0.0843,thrC<br />
97,18,3.9165,133.54,-1.0268,0.0928,yaaX<br />
257,19,4.0733,132.55,-0.4117,0.1089,yaaA<br />
475,20,4.0413,126.46,+0.6781,0.1242,yaaJ<br />
316,20,4.0395,128.99,-0.2165,0.0728,talB<br />
<br />
<font color=red>[Part of this file has been deleted for brevity]</font><br />
<br />
169,20,4.0001,124.90,+0.0231,0.0710,yjjX<br />
214,20,3.9937,129.77,-0.3813,0.0374,ytjC<br />
288,20,4.1421,132.58,-0.3628,0.1111,rob<br />
156,20,4.0627,126.72,-0.0442,0.0705,creA<br />
228,20,4.0471,131.94,-0.1408,0.0789,creB<br />
473,20,4.0254,128.01,+0.0023,0.0677,creC<br />
449,20,4.0871,128.66,+0.2082,0.0980,creD<br />
237,20,4.0729,132.54,-0.4970,0.0675,arcA<br />
45,15,3.5800,123.27,+0.7533,0.0222,yjjY<br />
227,20,4.0283,128.63,-0.0031,0.0573,yjtD<br />
</td></tr></table>
<br />
<br />

</p>

<h2>Data files</h2>

<p>
None.
</p>

<h2>Notes</h2>

<p>
None.
</p>

<h2>References</h2>

<pre>
   Lobry, JR. and Gautier, C. (1994) Hydrophobicity, expressivity and
      aromaticity are the major trends of amino-acid usage in 999 Escherichia
      coli chromosome-encoded genes, Nucleic Acids Res, 22:3174-3180.a

   Zavala A et al. (2002) Trends in codon and amino acid usage in Thermotoga
      maritima J Mol Evol. 54(5):563-8.

   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="gcodoncompiler.html">gcodoncompiler</a></td>
<td>Calculate various kinds of amino acid and codon usage data</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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