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date Fri, 26 Jun 2015 05:21:44 -0400
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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gaminoinfo </TITLE>
6 </HEAD>
7 <BODY BGCOLOR="#FFFFFF" text="#000000">
8
9
10
11 <table align=center border=0 cellspacing=0 cellpadding=0>
12 <tr><td valign=top>
13 <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>
14 </td>
15 <td align=left valign=middle>
16 <b><font size="+6">
17 gaminoinfo
18 </font></b>
19 </td></tr>
20 </table>
21 <br>&nbsp;
22 <p>
23
24
25 <!--END OF HEADER-->
26
27
28
29
30
31
32 <H2> Function </H2>
33 Prints out basic amino acid sequence statistics
34 <!--
35 DON'T WRITE ANYTHING HERE.
36 IT IS DONE FOR YOU.
37 -->
38
39
40
41
42 <H2>Description</H2>
43 <p>
44 gaminoinfo prints out basic compositional statistics of the given amino<br />
45 acid sequence in a human readble manner. The calculated values are molecular<br />
46 weight, number of residues, average residue weight, charge, isoelectric<br />
47 point, number/mole/Dayhoffstat of each amino acid, and percentage of<br />
48 Tiny (A+C+G+S+T), Small (A+B+C+D+G+N+P+S+T+V), Aliphatic (I+L+V),<br />
49 Armoatic (F+H+W+Y), Non-polar (A+C+F+G+I+L+M+P+V+W+Y),<br />
50 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 />
51 Acidic (B+D+E+Z) reidues.<br />
52 <br />
53 <br />
54 G-language SOAP service is provided by the<br />
55 Institute for Advanced Biosciences, Keio University.<br />
56 The original web service is located at the following URL:<br />
57 <br />
58 http://www.g-language.org/wiki/soap<br />
59 <br />
60 WSDL(RPC/Encoded) file is located at:<br />
61 <br />
62 http://soap.g-language.org/g-language.wsdl<br />
63 <br />
64 Documentation on G-language Genome Analysis Environment methods are<br />
65 provided at the Document Center<br />
66 <br />
67 http://ws.g-language.org/gdoc/<br />
68 <br />
69
70 </p>
71
72 <H2>Usage</H2>
73
74 Here is a sample session with gaminoinfo
75
76 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
77
78 % gaminoinfo tsw:hbb_human
79 Prints out basic amino acid sequence statistics
80 AAINDEX entry output file [hbb_human.gaminoinfo]:
81
82 </pre></td></tr></table>
83
84 Go to the <a href="#input">input files</a> for this example<br>
85 Go to the <a href="#output">output files</a> for this example<br><br>
86
87 <h2>Command line arguments</h2>
88
89 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
90 <tr bgcolor="#FFFFCC">
91 <th align="left">Qualifier</th>
92 <th align="left">Type</th>
93 <th align="left">Description</th>
94 <th align="left">Allowed values</th>
95 <th align="left">Default</th>
96 </tr>
97
98 <tr bgcolor="#FFFFCC">
99 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
100 </tr>
101
102 <tr bgcolor="#FFFFCC">
103 <td>[-sequence]<br>(Parameter 1)</td>
104 <td>seqall</td>
105 <td>Protein sequence(s) filename and optional format, or reference (input USA)</td>
106 <td>Readable sequence(s)</td>
107 <td><b>Required</b></td>
108 </tr>
109
110 <tr bgcolor="#FFFFCC">
111 <td>[-outfile]<br>(Parameter 2)</td>
112 <td>outfile</td>
113 <td>AAINDEX entry output file</td>
114 <td>Output file</td>
115 <td><i>&lt;*&gt;</i>.gaminoinfo</td>
116 </tr>
117
118 <tr bgcolor="#FFFFCC">
119 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
120 </tr>
121
122 <tr>
123 <td colspan=5>(none)</td>
124 </tr>
125
126 <tr bgcolor="#FFFFCC">
127 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
128 </tr>
129
130 <tr>
131 <td colspan=5>(none)</td>
132 </tr>
133
134 </table>
135
136
137 <h2 id="input">Input file format</h2>
138
139 <p>
140 The database definitions for following commands are available at<br />
141 http://soap.g-language.org/kbws/embossrc<br />
142 <br />
143 gaminoinfo reads one or more protein sequences.<br />
144 <br />
145
146 </p>
147
148 <h2 id="output">Output file format</h2>
149
150 <p>
151 The output from gaminoinfo is to a plain text file.<br />
152 <br />
153 File: hbb_human.gaminoinfo<br />
154 <br />
155 <table width="90%"><tr><td bgcolor="#CCFFCC">
156 Sequence: P68871<br />
157 AminoInfo of from 1 to 158<br />
158 <br />
159 Molecular weight = 19309.27 Residues = 158<br />
160 Average Weight = 122.21 Charge = 3.5<br />
161 Isoelectric Point = 7.4065<br />
162 Residue Number Mole% DayhoffStat<br />
163 <br />
164 = 1 0.633 0.000<br />
165 > = 1 0.633 0.000<br />
166 A = Ala 16 10.127 1.178<br />
167 B = Asx 2 1.266 0.000<br />
168 C = Cys 2 1.266 0.436<br />
169 D = Asp 7 4.430 0.806<br />
170 E = Glu 8 5.063 0.844<br />
171 F = Phe 8 5.063 1.406<br />
172 G = Gly 13 8.228 0.980<br />
173 H = His 11 6.962 3.481<br />
174 K = Lys 11 6.962 1.055<br />
175 L = Leu 18 11.392 1.540<br />
176 M = Met 3 1.899 1.117<br />
177 N = Asn 7 4.430 1.030<br />
178 P = Pro 7 4.430 0.852<br />
179 Q = Gln 3 1.899 0.487<br />
180 R = Arg 3 1.899 0.387<br />
181 S = Ser 5 3.165 0.452<br />
182 T = Thr 7 4.430 0.726<br />
183 U = Sec 1 0.633 0.000<br />
184 V = Val 18 11.392 1.726<br />
185 W = Trp 2 1.266 0.974<br />
186 Y = Tyr 3 1.899 0.558<br />
187 _ = 1 0.633 0.000<br />
188 <br />
189 Property Residues Number Mole%<br />
190 Tiny (A+C+G+S+T) 43 27.215<br />
191 Small (A+B+C+D+G+N+P+S+T+V) 84 53.165<br />
192 Aliphatic (I+L+V) 36 22.785<br />
193 Aromatic (F+H+W+Y) 24 15.190<br />
194 Non-polar (A+C+F+G+I+L+M+P+V+W+Y) 90 56.962<br />
195 Polar (D+E+H+K+N+Q+R+S+T+Z) 62 39.241<br />
196 Charged (B+D+E+H+K+R+Z) 42 26.582<br />
197 Basic (H+K+R) 25 15.823<br />
198 Acidic (B+D+E+Z) 17 10.759<br />
199 </pre></td></tr></table>
200
201 </p>
202
203 <h2>Data files</h2>
204
205 <p>
206 None.
207 </p>
208
209 <h2>Notes</h2>
210
211 <p>
212 None.
213 </p>
214
215 <h2>References</h2>
216
217 <pre>
218 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
219 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
220 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
221
222 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
223 large-scale analysis of high-throughput omics data, J. Pest Sci.,
224 31, 7.
225
226 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
227 Analysis Environment with REST and SOAP Web Service Interfaces,
228 Nucleic Acids Res., 38, W700-W705.
229
230 </pre>
231
232 <h2>Warnings</h2>
233
234 <p>
235 None.
236 </p>
237
238 <h2>Diagnostic Error Messages</h2>
239
240 <p>
241 None.
242 </p>
243
244 <h2>Exit status</h2>
245
246 <p>
247 It always exits with a status of 0.
248 </p>
249
250 <h2>Known bugs</h2>
251
252 <p>
253 None.
254 </p>
255
256 <h2>See also</h2>
257
258 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
259 <th>Description</th></tr>
260
261 <tr>
262 <td><a href="gaaui.html">gaaui</a></td>
263 <td>Calculates various indece of amino acid usage</td>
264 </tr><tr>
265 <td><a href="gcodoncompiler.html">gcodoncompiler</a></td>
266 <td>Calculate various kinds of amino acid and codon usage data</td>
267 </tr>
268
269 </table>
270
271 <h2>Author(s)</h2>
272
273 <pre>
274 Hidetoshi Itaya (celery@g-language.org)
275 Institute for Advanced Biosciences, Keio University
276 252-0882 Japan
277
278 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
279 Institute for Advanced Biosciences, Keio University
280 252-0882 Japan</pre>
281
282 <h2>History</h2>
283
284 2012 - Written by Hidetoshi Itaya
285
286 <h2>Target users</h2>
287
288 This program is intended to be used by everyone and everything, from
289 naive users to embedded scrips.
290
291 <h2>Comments</h2>
292
293 None.
294