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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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goligomersearch
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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>
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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>[-oligomer]<br>(Parameter 2)</td>
<td>string</td>
<td>Oligomer to search</td>
<td>Any string</td>
<td> </td>
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<td>[-outfile]<br>(Parameter 3)</td>
<td>outfile</td>
<td>Program compseq output file</td>
<td>Output file</td>
<td><i><*></i>.goligomersearch</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>-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>
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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 />
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 />
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</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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