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<TITLE> EMBOSS: gpalindrome </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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gpalindrome
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<H2> Function </H2>
Searches palindrome sequences
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<H2>Description</H2>
<p>
gpalindrome searches for palindrome sequences in the genome.<br />
Search parameters can be changed for more efficient searches, and g-t<br />
matching can be specified by passing the "-gtmatch" qualifier.<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 gpalindrome
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% gpalindrome refseqn:NC_000913
Searches palindrome sequences
Program compseq output file [nc_000913.gpalindrome]:
</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>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>Program compseq output file</td>
<td>Output file</td>
<td><i><*></i>.gpalindrome</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>-shortest</td>
<td>integer</td>
<td>Shortest palindrome to search</td>
<td>Any integer value</td>
<td>4</td>
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<td>-loop</td>
<td>integer</td>
<td>Longest stem loop to allow</td>
<td>Any integer value</td>
<td>0</td>
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<td>-gtmatch</td>
<td>boolean</td>
<td>If 1, allows g-t match</td>
<td>Boolean value Yes/No</td>
<td>No</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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</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 />
gpalindrome reads one or more nucleotide sequences.<br />
<br />
</p>
<h2 id="output">Output file format</h2>
<p>
The output from gpalindrome is to a plain text file.<br />
<br />
File: nc_000913.gpalindrome<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
Length, start, end, sequence<br />
4,16,18,tg ca<br />
4,27,29,at at<br />
4,44,46,tt aa<br />
4,67,69,ag ct<br />
4,97,99,aa tt<br />
4,99,101,tt aa<br />
10,100,108,taaaa tttta<br />
4,132,134,tt aa<br />
<br />
<font color=red>[Part of this file has been deleted for brevity]</font><br />
<br />
4,4639484,4639486,tg ca<br />
6,4639487,4639491,aag ctt<br />
4,4639495,4639497,cg cg<br />
4,4639506,4639508,ca tg<br />
6,4639552,4639556,gtc gac<br />
4,4639607,4639609,tg ca<br />
4,4639619,4639621,tg ca<br />
4,4639621,4639623,ca tg<br />
4,4639625,4639627,at at<br />
4,4639637,4639639,at at<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="gconsensusz.html">gconsensusz</a></td>
<td>Calculate consensus in given array of sequences</td>
</tr><tr>
<td><a href="gdistincc.html">gdistincc</a></td>
<td>Calculates the distance between two loci in circular chromosomes</td>
</tr><tr>
<td><a href="gseqinfo.html">gseqinfo</a></td>
<td>Prints out basic nucleotide sequence statistics</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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