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<TITLE> EMBOSS: gnucleotideperiodicity </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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gnucleotideperiodicity
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<H2> Function </H2>
Checks the periodicity of certain oligonucleotides
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<H2>Description</H2>
<p>
gnucleotideperiodicity checks the periodicity of certain nucleotide<br>
(best known with AA dinucleotide). Bacteria and archaebacteria are<br>
known to show periodicity of ApA dinucleotides at about 11bp and 10bp.<br>
Lower eukaryotes also show periodicity but higher eukaryotes do not.<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 gnucleotideperiodicity
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% gnucleotideperiodicity refseqn:NC_000913
Checks the periodicity of certain oligonucleotides
Program compseq output file (optional) [nc_000913.gnucleotideperiodicity]:
</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>
Example 2
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>?
% gnucleotideperiodicity refseqn:NC_000913 -plot -graph png
Checks the periodicity of certain oligonucleotides
Created gnucleotideperiodicity.1.png
</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>-graph</td>
<td>xygraph</td>
<td>Graph type</td>
<td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td>
<td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
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<td>-outfile</td>
<td>outfile</td>
<td>Program compseq output file (optional)</td>
<td>Output file</td>
<td><i><*></i>.gnucleotideperiodicity</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>-format</td>
<td>string</td>
<td>Output file format. Dependent on 'convert' command</td>
<td>Any string</td>
<td>png</td>
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<td>-window</td>
<td>integer</td>
<td>Window size to seek periodicity</td>
<td>Any integer value</td>
<td>50</td>
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<td>-nucleotide</td>
<td>string</td>
<td>Nucleotide to search</td>
<td>Any string</td>
<td>aa</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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<td>-plot</td>
<td>toggle</td>
<td>Include to plot result</td>
<td>Toggle value Yes/No</td>
<td>No</td>
</tr>
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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 />
gnucleotideperiodicity reads one or more nucleotide sequences.<br />
<br />
</p>
<h2 id="output">Output file format</h2>
<p>
The output from gnucleotideperiodicity is to a plain text file or the EMBOSS graphics device.<br />
<br />
File: nc_000913.gnucleotideperiodicity<br />
<br /></td></tr></table>
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
window,value<br />
0,35134<br />
1,30121<br />
2,25409<br />
3,23508<br />
4,25830<br />
5,25136<br />
6,25658<br />
7,28279<br />
<br />
<font color=red>[Part of this file has been deleted for brevity]</font><br />
<br />
40,28042<br />
41,25892<br />
42,25968<br />
43,28240<br />
44,25841<br />
45,25591<br />
46,27788<br />
47,25832<br />
48,25427<br />
49,0<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="gkmertable.html">gkmertable</a></td>
<td>Create an image showing all k-mer abundance within a sequence</td>
</tr><tr>
<td><a href="goligomercounter.html">goligomercounter</a></td>
<td>Counts the number of given oligomers in a sequence</td>
</tr><tr>
<td><a href="goligomersearch.html">goligomersearch</a></td>
<td>Searches oligomers in given sequence</td>
</tr><tr>
<td><a href="gsignature.html">gsignature</a></td>
<td>Calculate oligonucleotide usage (genomic signature)</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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