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<TITLE> EMBOSS: gldabias </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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gldabias
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<H2> Function </H2>
Calculate strand bias of bacterial genome using linear discriminant
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<H2>Description</H2>
<p>
gldabias calculates strand bias of bacterial genome using linear<br />
discriminant analysis (LDA), as proposed in Reference 1. The basic idea is<br />
to use composition data of genes to train and predict the strand of genes<br />
residing either on the leading or the lagging strand. For computational<br />
efficiency, this method trans and predicts the strands at putative<br />
replication origin as reported by the rep_ori_ter() method. This usually<br />
results in maximum predictability of LDA within bacterial genomes.<br />
Data to use for LDA can be chosen from "base", "codonbase", "codon", and<br />
"amino", with -variable option.<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 gldabias
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% gldabias refseqn:NC_000913
Calculate strand bias of bacterial genome using linear discriminant
analysis (LDA)
Program compseq output file [nc_000913.gldabias]:
</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>
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<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>
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<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
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<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>
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<td>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>Program compseq output file</td>
<td>Output file</td>
<td><i><*></i>.gldabias</td>
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<th align="left" colspan=5>Additional (Optional) qualifiers</th>
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<td colspan=5>(none)</td>
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<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
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<td>-coefficients</td>
<td>integer</td>
<td>Show LDA coefficients</td>
<td>Any integer value</td>
<td>0</td>
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<td>-variable</td>
<td>selection</td>
<td>Data to use for LDA. Either 'base', 'codonbase', 'codon', or 'amino'</td>
<td>Choose from selection list of values</td>
<td>codon</td>
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<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>
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<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 />
gldabias reads one or more nucleotide sequences.<br />
<br />
</p>
<h2 id="output">Output file format</h2>
<p>
The output from gldabias is to a plain text file.<br />
<br />
File: nc_000913.gldabias<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913 LDA-BIAS: 0.742533<br />
</td></tr></table>
</p>
<h2>Data files</h2>
<p>
None.
</p>
<h2>Notes</h2>
<p>
None.
</p>
<h2>References</h2>
<pre>
Rocha EPC et al. (1999) "Universal replication biases in bacteria",
Molecular Microbiology, 32(1):11-16
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="ggcsi.html">ggcsi</a></td>
<td>GC Skew Index: an index for strand-specefic mutational bias</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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