Mercurial > repos > ktnyt > gembassy

diff GEMBASSY-1.0.3/doc/html/genc.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/genc.html	Fri Jun 26 05:19:29 2015 -0400
@@ -0,0 +1,1 @@
+<!--START OF HEADER - DON'T ALTER -->

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


<!--END OF HEADER-->






<H2> Function </H2>
   Calculate the effective number of codons (Nc)
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>Description</H2>
<p>
   genc calculates the effective number of codons (ENC|Nc). ENC is a measure<br />
   for species-independent codon usage bias. Some measures including CAI are<br />
   species-dependent as optimal codons differ. ENC assigns a gene a number<br />
   between 20 to 61 where 20 indicates that one codon is used for each amino<br />
   acid and 61 indicates that each codon is used equally throughout the<br />
   protein sequence.<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 genc

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

% genc refseqn:NC_000913
Calculate the effective number of codons (Nc)
Codon usage output file [nc_000913.genc]: 

</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>Codon usage output file</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.genc</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>-translate</td>
<td>boolean</td>
<td>Include when translates using standard codon table</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-delkey</td>
<td>string</td>
<td>Regular expression to delete key (i.e. amino acids and nucleotides)</td>
<td>Any string</td>
<td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</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 />
   genc reads one or more nucleotide sequences.<br />
<br />

</p>

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

<p>
   The output from genc is to a plain text file.<br />
<br />
   File: nc_000913.genc<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
enc,gene<br />
,thrL<br />
48.41,thrA<br />
54.13,thrB<br />
46.18,thrC<br />
51.65,yaaX<br />
45.71,yaaA<br />
48.54,yaaJ<br />
36.83,talB<br />
<br />
<font color=red>[Part of this file has been deleted for brevity]</font><br />
<br />
51.43,yjjX<br />
46.61,ytjC<br />
49.83,rob<br />
47.74,creA<br />
50.63,creB<br />
51.39,creC<br />
48.42,creD<br />
41.53,arcA<br />
61,yjjY<br />
53.63,yjtD<br />
</td></tr></table>

</p>

<h2>Data files</h2>

<p>
None.
</p>

<h2>Notes</h2>

<p>
None.
</p>

<h2>References</h2>

<pre>
   Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
      usage bias, J Mol Evol, 47(3):268-74.

   Wright F. (1990) The 'effective number of codons' used in a gene, Gene,
      87:23-29.

   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="gew.html">gew</a></td>
<td>Calculate a measure of synonymous codon usage evenness (Ew)</td>
</tr><tr>
<td><a href="gfop.html">gfop</a></td>
<td>Calculate the frequency of optimal codons (Fop)</td>
</tr><tr>
<td><a href="gscs.html">gscs</a></td>
<td>Calculates the scaled chi-square</td>
</tr><tr>
<td><a href="gwvalue.html">gwvalue</a></td>
<td>Calculate the 'relative adaptiveness of each codon' (W)</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