Mercurial > repos > ktnyt > gembassy

view GEMBASSY-1.0.3/doc/html/gb1.html @ 1:84a17b3fad1f draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ktnyt
date Fri, 26 Jun 2015 05:20:29 -0400
parents 8300eb051bea
children
line wrap: on
line source

<!--START OF HEADER - DON'T ALTER -->

<HTML>
<HEAD>
  <TITLE> EMBOSS: gb1 </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">
gb1
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<!--END OF HEADER-->






<H2> Function </H2>
   Calculate strand bias of bacterial genome using B1 index
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>Description</H2>
<p>
   gb1 calculates the strand bias of bacterial genome using B1 index,<br />
   first proposed by Lobry and Sueoka (2002), and further extended by<br />
   Rocha et al. (2006). Basic idea of B1 index is to calculate the<br />
   distance between the two strands, when the leading and lagging strands<br />
   are plotted in a coordinate system with axes representing G/(G+C) and<br />
   A/(A+T), using the third codon position of genes. This index measures the<br />
   degree of replication-induced bias from Chargaff's second parity rule.<br />
   Rocha et al. modified B1 index to only use >fourfold degenerate codons,<br />
   and to use T/(A+T) in place of A/(A+T).<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 gb1

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

% gb1 refseqn:NC_000913
Calculate strand bias of bacterial genome using B1 index
Program compseq output file [nc_000913.gb1]: 

</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>Program compseq output file</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.gb1</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>-method</td>
<td>selection</td>
<td>Choose method of 'lobry' or 'rocha'</td>
<td>Choose from selection list of values</td>
<td>rocha</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 />
   gb1 reads one or more nucleotide sequences.<br />
<br />

</p>

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

<p>
   The output from gb1 is to a plain text file.<br />
<br />
   File: nc_000913.gb1<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913 B1: 0.0630702874711314<br />
</td></tr></table>

</p>

<h2>Data files</h2>

<p>
None.
</p>

<h2>Notes</h2>

<p>
None.
</p>

<h2>References</h2>

<pre>
   Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in
      bacteria, Genome Biology, 3(10):0058

   Rocha EPC et al. (2006) Similar compositional biases are caused by very
      different mutational effects, Genome Research, 16:1537-1547

   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="gb2.html">gb2</a></td>
<td>Calculate strand bias of bacterial genome using B2 index</td>
</tr><tr>
<td><a href="gdeltagcskew.html">gdeltagcskew</a></td>
<td>Calculate strand bias of bacterial genome using delta GC skew</td>
</tr><tr>
<td><a href="ggcsi.html">ggcsi</a></td>
<td>GC Skew Index: an index for strand-specefic mutational bias</td>
</tr><tr>
<td><a href="gldabias.html">gldabias</a></td>
<td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</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.