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  <TITLE> EMBOSS: goligomersearch </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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<b><font size="+6">
goligomersearch
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<br>&nbsp;
<p>


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<H2> Function </H2>
   Searches oligomers in given sequence
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<H2>Description</H2>
<p>
   goligomersearch searches for the given oligomer in given sequence. Oligomer<br />
   can be specified using degenerate nucleotide alphabet, or by regular<br />
   expressions. Performance is optimized for fast searching.<br />
   This method changes the returning value according to the given options.<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 goligomersearch

<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>

% goligomersearch refseqn:NC_000913 atgcatgc
Searches oligomers in given sequence
Program compseq output file [nc_000913.goligomersearch]: 

</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>[-oligomer]<br>(Parameter 2)</td>
<td>string</td>
<td>Oligomer to search</td>
<td>Any string</td>
<td>&nbsp;</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>[-outfile]<br>(Parameter 3)</td>
<td>outfile</td>
<td>Program compseq output file</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.goligomersearch</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>-return</td>
<td>selection</td>
<td>'position' to return list of positions where oligomers are found, 'oligo' to return list of oligomers found ordered by positions, 'both' to return a hash with positions as keys and oligomers as values, 'distribution' to return four values about the distribution of given oligomer</td>
<td>Choose from selection list of values</td>
<td>position</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 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 />
   goligomersearch reads one or more nucleotide sequences.<br />
<br />

</p>

<h2 id="output">Output file format</h2>

<p>
   The output from goligomersearch is to a plain text file.<br />
<br />
   File: nc_000913.goligomersearch<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913 Oligomer: atgcatgc Return: 147018,366819,653138,863326,1288615,1627117,2111200,2246695,2697278,2750962,2826906,2882353,2998362,3022134,3346029,3477018,3629113,3842819,3958304,3982183,4013480,4285578,4474663,4484501,4499080,4604562,4638391<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="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="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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