Mercurial > repos > ktnyt > gembassy

view GEMBASSY-1.0.3/doc/html/gbui.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: gbui </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">
gbui
</font></b>
</td></tr>
</table>
<br>&nbsp;
<p>


<!--END OF HEADER-->






<H2> Function </H2>
   Calculates base usage indices for protein-coding sequences
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
-->




<H2>Description</H2>
<p>
   gbui calculates base usage indices of protein-coding sequences (excluding<br />
   start and stop codons) for each gene. Indices calculated are as follows,<br />
      acgt: Total bumber of bases (A+T+G+C)<br />
      ryr:  Purine/Pyrimidine ratio (A+G)/(T+C)<br />
      gcc:  G+C content (G+C)/(A+T+G+C)<br />
      Hgc:  entropy of G+C content (G+C)/(A+T+G+C)<br />
      gcs:  GC skew (C-G)/(C+G)<br />
      ats:  AT skew (A-T)/(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 gbui

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

% gbui refseqn:NC_000913
Calculates base usage indices for protein-coding sequences
Program compseq output file [nc_000913.gbui]: 

</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>.gbui</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 translating using standard codon table</td>
<td>Boolean value Yes/No</td>
<td>No</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-position</td>
<td>list</td>
<td>Codon position</td>
<td><table><tr><td>all</td> <td><i>(Assess overall base usage of the gene)</i></td></tr><tr><td>1</td> <td><i>(Assess base usage at 1st position of codons)</i></td></tr><tr><td>2</td> <td><i>(Assess base usage at 2nd position of codons)</i></td></tr><tr><td>3</td> <td><i>(Assess base usage at 3rd position of codons)</i></td></tr></table></td>
<td>all</td>
</tr>

<tr bgcolor="#FFFFCC">
<td>-delkey</td>
<td>string</td>
<td>Regular expression to delete key</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 />
   gbui reads one or more nucleotide sequences.<br />
<br />

</p>

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

<p>
   The output from gbui is to a plain text file.<br />
<br />
   File: nc_000913.gbui<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: NC_000913<br />
acgt,ryr,gcc,Hgc,gcs,ats,gene<br />
60,0.9355,0.5333,0.9968,+0.3750,+0.3571,thrL<br />
2457,1.0206,0.5311,0.9972,-0.0575,-0.0434,thrA<br />
927,1.0973,0.5653,0.9877,-0.1183,-0.0471,thrB<br />
1281,1.0795,0.5301,0.9974,-0.0692,+0.0033,thrC<br />
291,1.0638,0.5430,0.9947,+0.0506,+0.1278,yaaX<br />
771,1.0615,0.4994,1.0000,-0.0182,+0.0415,yaaA<br />
1425,0.8363,0.5347,0.9965,-0.0315,-0.2278,yaaJ<br />
948,1.1303,0.5222,0.9986,-0.0263,+0.0993,talB<br />
<br />
<font color=red>[Part of this file has been deleted for brevity]</font><br />
<br />
507,1.0444,0.5661,0.9874,-0.1080,-0.0909,yjjX<br />
642,1.1472,0.5654,0.9876,-0.0909,+0.0394,ytjC<br />
864,0.9636,0.5347,0.9965,+0.0087,-0.0299,rob<br />
468,1.1273,0.4936,0.9999,-0.1169,+0.0042,creA<br />
684,1.0118,0.5556,0.9911,-0.0579,-0.0592,creB<br />
1419,1.0655,0.5398,0.9954,-0.1018,-0.0505,creC<br />
1347,1.0660,0.4974,1.0000,-0.1433,-0.0783,creD<br />
711,1.0850,0.5134,0.9995,-0.0082,+0.0751,arcA<br />
135,0.8493,0.4370,0.9885,+0.2203,+0.0263,yjjY<br />
681,1.1415,0.5007,1.0000,-0.0792,+0.0529,yjtD<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="gdinuc.html">gdinuc</a></td>
<td>Calculates dinucleotide usage</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>