|
0
|
1 <!--START OF HEADER - DON'T ALTER -->
<HTML>
<HEAD>
<TITLE> EMBOSS: gicdi </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">
gicdi
</font></b>
</td></tr>
</table>
<br>
<p>
<!--END OF HEADER-->
<H2> Function </H2>
Calculates the intrinsic codon deviation index (ICDI)
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->
<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 gicdi
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% gicdi refseqn:NC_000913
Calculates the intrinsic codon deviation index (ICDI)
Codon usage output file [nc_000913.gicdi]:
</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>.gicdi</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 />
gicdi reads one or more nucleotide sequences.<br />
<br />
</p>
<h2 id="output">Output file format</h2>
<p>
The output from gicdi is to a plain text file.<br />
<br />
File: nc_000913.gicdi<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
icdi,gene<br />
0.8192,thrL<br />
0.1258,thrA<br />
0.1127,thrB<br />
0.1689,thrC<br />
0.3099,yaaX<br />
0.2030,yaaA<br />
0.1600,yaaJ<br />
0.3533,talB<br />
<br />
<font color=red>[Part of this file has been deleted for brevity]</font><br />
<br />
0.2203,yjjX<br />
0.2719,ytjC<br />
0.1377,rob<br />
0.2647,creA<br />
0.1944,creB<br />
0.1733,creC<br />
0.1926,creD<br />
0.2728,arcA<br />
0.5171,yjjY<br />
0.2434,yjtD<br />
</td></tr></table>
</p>
<h2>Data files</h2>
<p>
None.
</p>
<h2>Notes</h2>
<p>
None.
</p>
<h2>References</h2>
<pre>
Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
usage bias, J Mol Evol, 47(3):268-74.
Freire-Picos MA et al. (1994) Codon usage in Kluyveromyces lactis and in
yeast cytochrome c-encoding genes, Gene, 139:43-49.
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="gcbi.html">gcbi</a></td>
<td>Calculates the codon bias index (CBI)</td>
</tr><tr>
<td><a href="gdeltaenc.html">gdelta_enc</a></td>
<td>Calculate the codon usage bias related to translation optimization (delta ENC)</td>
</tr><tr>
<td><a href="gsvalue.html">gs_value</a></td>
<td>Calculate the strength of selected codon usage bias (S)</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> |
