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<TITLE> EMBOSS: gaminoinfo </TITLE>
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<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>
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gaminoinfo
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<H2> Function </H2>
Prints out basic amino acid sequence statistics
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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>
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<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>
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<th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
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<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><*></i>.gaminoinfo</td>
</tr>
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<th align="left" colspan=5>Additional (Optional) qualifiers</th>
</tr>
<tr>
<td colspan=5>(none)</td>
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<th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
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<tr>
<td colspan=5>(none)</td>
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<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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