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<TITLE> EMBOSS: greporiter </TITLE>
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greporiter
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<H2> Function </H2>
Get the positions of replication origin and terminus
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<H2>Description</H2>
<p>
greporiter returns the positions of replication origin and terminus<br />
in bacterial genomes by several means. <br />
<br />
1. Use of databases<br />
By default, grep_ori_ter tries to retrieve the position of replication<br />
origin in DoriC Gao and Zhang (2007) database, and the position of<br />
replication terminus from the supplemental data provided in<br />
Kono et al. (2011).<br />
If the position of origin cannot be found in the database, but "rep_origin" <br />
feature is available, center position within this feature is used for<br />
origin. <br />
<br />
2. Oriloc<br />
Using -orilocoption, you can predict the replication origin and <br />
terminus using the popular Oriloc program developed by Lobry et al. <br />
available as part of the SeqinR package Frank and Lobry (2000).<br />
<br />
3. Use GC skew shift-point<br />
If the positions of origin or terminus cannot be found in the databases,<br />
grep_ori_ter automatically calls find_ori_ter() method to predict the <br />
positions using GC skew shift-points at one-base-pair resolution.<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>
Here is a sample session with greporiter
<table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
% greporiter refseqn:NC_000913
Get the positions of replication origin and terminus
Output file [nc_000913.greporiter]:
</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>Output file name</td>
<td>Output file</td>
<td><i><*></i>.greporiter</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>-oriloc</td>
<td>boolean</td>
<td>Include Oriloc for prediction</td>
<td>Boolean value Yes/No</td>
<td>No</td>
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<td>-gcskew</td>
<td>boolean</td>
<td>Include to use GC skew shift-point for prediction</td>
<td>Boolean value Yes/No</td>
<td>No</td>
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<td>-difthreshold</td>
<td>integer</td>
<td>Distance between the GC skew shift point and predicted dif site expressed as the precentage of genome size, used as a threshold to retrieve dif sequence from the database</td>
<td>Any integer value</td>
<td>0</td>
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<td>-dbonly</td>
<td>boolean</td>
<td>Include to only use values available in databases and to suppress prediction</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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<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 />
greporiter reads one or more nucleotide sequences.<br />
<br />
</p>
<h2 id="output">Output file format</h2>
<p>
The output from greporiter is to a plain text file.<br />
<br />
File: nc_000913.greporiter<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913 Origin: 3923881 Terminus: 1550412<br />
</td></tr></table>
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<h2>Data files</h2>
<p>
None.
</p>
<h2>Notes</h2>
<p>
None.
</p>
<h2>References</h2>
<pre>
Gao F and Zhang CT (2007) DoriC: a database of oriC regions in bacterial
genomes, Bioinformatics, 23(14):1866-1867
Kono N et al. (2011) Comprehensive prediction of chromosome dimer resolution
sites in bacterial genomes, BMC Genomics, 12(1):19
Frank AC and Lobry JR (2000) "Oriloc: prediction of replication boundaries
in unannotated bacterial chromosomes", Bioinformatics, 16(6):560-561
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>
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<td><a href="gfindoriter.html">gfindoriter</a></td>
<td>Predicts the replication origin and terminus in bacterial</td>
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<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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