Mercurial > repos > ktnyt > gembassy

diff GEMBASSY-1.0.3/doc/html/greporiter.html @ 0:8300eb051bea draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
parents
children
line wrap: on
line diff
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/GEMBASSY-1.0.3/doc/html/greporiter.html	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,1 @@
+<!--START OF HEADER - DON'T ALTER -->

<HTML>
<HEAD>
  <TITLE> EMBOSS: greporiter </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">
greporiter
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<!--END OF HEADER-->






<H2> Function </H2>
   Get the positions of replication origin and terminus
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<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 />

</p>

<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>

<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>[-outfile]<br>(Parameter 2)</td>
<td>outfile</td>
<td>Output file name</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.greporiter</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>-oriloc</td>
<td>boolean</td>
<td>Include Oriloc for prediction</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<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>
</tr>

<tr bgcolor="#FFFFCC">
<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>
</tr>

<tr bgcolor="#FFFFCC">
<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>
</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 />
   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>

</p>

<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>

<tr>
<td><a href="gfindoriter.html">gfindoriter</a></td>
<td>Predicts the replication origin and terminus in bacterial</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>
\ No newline at end of file