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

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


<!--END OF HEADER-->






<H2> Function </H2>
   Prints out basic amino acid sequence statistics
<!--
DON'T WRITE ANYTHING HERE.
IT IS DONE FOR YOU.
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<H2>Description</H2>
<p>
   gaminoinfo prints out basic compositional statistics of the given amino<br />
   acid sequence in a human readble manner. The calculated values are molecular<br />
   weight, number of residues, average residue weight, charge, isoelectric<br />
   point, number/mole/Dayhoffstat of each amino acid, and percentage of<br />
   Tiny (A+C+G+S+T), Small (A+B+C+D+G+N+P+S+T+V), Aliphatic (I+L+V),<br />
   Armoatic (F+H+W+Y), Non-polar (A+C+F+G+I+L+M+P+V+W+Y),<br />
   Polar (D+E+H+K+N+Q+R+S+T+Z), Charged (B+D+E+H+K+R+Z), Basic (H+K+R), and<br />
   Acidic (B+D+E+Z) reidues.<br />
  <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 gaminoinfo

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

% gaminoinfo tsw:hbb_human
Prints out basic amino acid sequence statistics
AAINDEX entry output file [hbb_human.gaminoinfo]: 

</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>Protein 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>AAINDEX entry output file</td>
<td>Output file</td>
<td><i>&lt;*&gt;</i>.gaminoinfo</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>
<td colspan=5>(none)</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 />
   gaminoinfo reads one or more protein sequences.<br />
<br />

</p>

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

<p>
   The output from gaminoinfo is to a plain text file.<br />
<br />
   File: hbb_human.gaminoinfo<br />
<br />
<table width="90%"><tr><td bgcolor="#CCFFCC">
Sequence: P68871<br />
AminoInfo of  from 1 to 158<br />
<br />
Molecular weight = 19309.27 Residues = 158<br />
Average Weight = 122.21 Charge = 3.5<br />
Isoelectric Point = 7.4065<br />
Residue         Number          Mole%               DayhoffStat<br />
<br />
 =             1               0.633                     0.000<br />
> =             1               0.633                     0.000<br />
A = Ala         16              10.127                    1.178<br />
B = Asx         2               1.266                     0.000<br />
C = Cys         2               1.266                     0.436<br />
D = Asp         7               4.430                     0.806<br />
E = Glu         8               5.063                     0.844<br />
F = Phe         8               5.063                     1.406<br />
G = Gly         13              8.228                     0.980<br />
H = His         11              6.962                     3.481<br />
K = Lys         11              6.962                     1.055<br />
L = Leu         18              11.392                    1.540<br />
M = Met         3               1.899                     1.117<br />
N = Asn         7               4.430                     1.030<br />
P = Pro         7               4.430                     0.852<br />
Q = Gln         3               1.899                     0.487<br />
R = Arg         3               1.899                     0.387<br />
S = Ser         5               3.165                     0.452<br />
T = Thr         7               4.430                     0.726<br />
U = Sec         1               0.633                     0.000<br />
V = Val         18              11.392                    1.726<br />
W = Trp         2               1.266                     0.974<br />
Y = Tyr         3               1.899                     0.558<br />
_ =             1               0.633                     0.000<br />
<br />
Property        Residues                Number          Mole%<br />
Tiny            (A+C+G+S+T)             43              27.215<br />
Small           (A+B+C+D+G+N+P+S+T+V)   84              53.165<br />
Aliphatic       (I+L+V)                 36              22.785<br />
Aromatic        (F+H+W+Y)               24              15.190<br />
Non-polar       (A+C+F+G+I+L+M+P+V+W+Y) 90              56.962<br />
Polar           (D+E+H+K+N+Q+R+S+T+Z)   62              39.241<br />
Charged         (B+D+E+H+K+R+Z)         42              26.582<br />
Basic           (H+K+R)                 25              15.823<br />
Acidic          (B+D+E+Z)               17              10.759<br />
</pre></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="gaaui.html">gaaui</a></td>
<td>Calculates various indece of amino acid usage</td>
</tr><tr>
<td><a href="gcodoncompiler.html">gcodoncompiler</a></td>
<td>Calculate various kinds of amino acid and codon usage data</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.
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