|
0
|
1 <!--START OF HEADER - DON'T ALTER -->
<HTML>
<HEAD>
<TITLE> EMBOSS: ggcsi </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">
ggcsi
</font></b>
</td></tr>
</table>
<br>
<p>
<!--END OF HEADER-->
<H2> Function </H2>
GC Skew Index: an index for strand-specific mutational bias
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->
<H2>Description</H2>
<p>
ggcsi calculates the GC Skew Index (GCSI) of the given circular bacterial<br />
genome. GCSI quantifies the degree of GC Skew. In other words, this index<br />
represents the degree of strand-specific mutational bias in bacterial<br />
genomes, caused by replicational selection. <br />
GCSI is calculated by the following formula:<br />
<br />
GCSI = sqrt((SA/6000) * (dist/600))<br />
<br />
where SA is the spectral amplitude of Fourier power spectrum at 1Hz,<br />
and dist is the normalized Euclidean distance between the vertices of <br />
cumulative GC skew.<br />
<br />
GCSI ranges from 0 (no observable skew) to 1 (strong skew), and Archaeal<br />
genomes that have multiple replication origins and therefore have no<br />
observable skew mostly have GCSI below 0.05. Escherichia coli genome has<br />
values around 0.10.<br />
<br />
Version 1 of GCSI required fixed number of windows (4096), but the new GCSI<br />
version 2 (also known as generalized GCSI: gGCSI) is invariant of the number<br />
of windows. GCSI version 1 is calculated as an arithmetic mean (as opposed<br />
to the geometric mean of gGCSI) of SR (spectral ratio, the signal-to-noise<br />
ratio of 1Hz power spectrum) and dist.<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 ggcsi
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% ggcsi refseqn:NC_000913
GC Skew Index: an index for strand-specific mutational bias
Program compseq output file [nc_000913.ggcsi]:
</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>Program compseq output file</td>
<td>Output file</td>
<td><i><*></i>.ggcsi</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>-gcsi</td>
<td>selection</td>
<td>GCSI version to use</td>
<td>Choose from selection list of values</td>
<td>2</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-window</td>
<td>integer</td>
<td>Number of windows. Must be a power of 2</td>
<td>Any integer value</td>
<td>4096</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-purine</td>
<td>boolean</td>
<td>Use purine skew for calculation</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-keto</td>
<td>boolean</td>
<td>Use keto skew for calculation</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-at</td>
<td>boolean</td>
<td>Use AT skew for calculation</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>
<tr bgcolor="#FFFFCC">
<td>-pval</td>
<td>boolean</td>
<td>Calculate p-value when GCSI version 2 is selected</td>
<td>Boolean value Yes/No</td>
<td>No</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>Input file format</h2>
<p id="input">
The database definitions for following commands are available at<br />
http://soap.g-language.org/kbws/embossrc<br />
<br />
ggcsi reads one or more nucleotide sequences.<br />
<br />
</p>
<h2 id="output">Output file format</h2>
<p>
The output from ggcsi is to a plain text file.<br />
<br />
File: nc_000913.ggcsi<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913 GCSI: 0.0966615833014818 SA: 487.218569030757 DIST: 69.037726<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="gb1.html">gb1</a></td>
<td>Calculate strand bias of bacterial genome using B1 index</td>
</tr><tr>
<td><a href="gb2.html">gb2</a></td>
<td>Calculate strand bias of bacterial genome using B2 index</td>
</tr><tr>
<td><a href="gdeltagcskew.html">gdeltagcskew</a></td>
<td>Calculate strand bias of bacterial genome using delta GC skew</td>
</tr><tr>
<td><a href="gldabias.html">gldabias</a></td>
<td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</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> |
