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<TITLE> EMBOSS: gkmertable </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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gkmertable
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<H2> Function </H2>
Create an image showing all k-mer abundance within a sequence
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<H2>Description</H2>
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gkmertable creates an image showing the abundance of all k-mers<br />
(oligonucleotides of length k) in a given sequence. For example, for<br />
tetramers (k=4), resulting image is composed of 4^4 = 256 boxes, each<br />
representing an oligomer. Oligomer name and abundance is written within<br />
these boxes, and abundance is also visualized with the box color, from<br />
white (none) to black (highly frequent).<br />
This k-mer table is alternatively known as the FCGR (frequency matrices<br />
extracted from Chaos Game Representation).<br />
Position of the oligomers can be recursively located as follows:<br />
For each letter in an oligomer, a box is subdivided into four quadrants, <br />
where A is upper left, T is lower right, G is upper right, and C is lower<br />
left.<br />
Therefore, oligomer ATGC is in the <br />
A = upper left quadrant<br />
T = lower right within the above quadrant<br />
G = upper right within the above quadrant<br />
C = lower left within the above quadrant<br />
More detailed documentation is available at <br />
http://www.g-language.org/wiki/cgr<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 />
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<H2>Usage</H2>
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
Here is a sample session with gkmertable
% gkmertable refseqn:NC_000913
Create an image showing all k-mer abundance within a sequence
Created gkmertable.1.png
Go to the input files for this example
Go to the output files for this example
</pre></td></tr></table>
<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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<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>-k</td>
<td>integer</td>
<td>Length of oligomer</td>
<td>Any integer value</td>
<td>6</td>
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<td>-goutfile</td>
<td>string</td>
<td>Output file for non interactive displays</td>
<td>Any string</td>
<td>gkmertable</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 />
gkmertable reads one or more nucleotide sequences.<br />
<br />
</p>
<h2 id="output">Output file format</h2>
<p>
The output from gkmertable is to an image file.<br />
</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="gnucleotideperiodicity.html">gnucleotideperiodicity</a></td>
<td>Checks the periodicity of certain oligonucleotides</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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