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1 <!--START OF HEADER - DON'T ALTER --> <HTML> <HEAD> <TITLE> EMBOSS: gkmertable </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"> gkmertable </font></b> </td></tr> </table> <br>&nbsp; <p> <!--END OF HEADER--> <H2> Function </H2> Create an image showing all k-mer abundance within a sequence <!-- DON'T WRITE ANYTHING HERE. IT IS DONE FOR YOU. --> <H2>Description</H2> <p> 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 /> </p> <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> <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"> <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>-format</td> <td>string</td> <td>Output file format. Dependent on 'convert' command</td> <td>Any string</td> <td>png</td> </tr> <tr bgcolor="#FFFFCC"> <td>-k</td> <td>integer</td> <td>Length of oligomer</td> <td>Any integer value</td> <td>6</td> </tr> <tr bgcolor="#FFFFCC"> <td>-goutfile</td> <td>string</td> <td>Output file for non interactive displays</td> <td>Any string</td> <td>gkmertable</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 /> 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. </BODY> </HTML>