Mercurial > repos > ktnyt > gembassy

comparison GEMBASSY-1.0.3/doc/html/gaaui.html @ 2:8947fca5f715 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ktnyt
date Fri, 26 Jun 2015 05:21:44 -0400
parents 84a17b3fad1f
children
comparison
equal deleted inserted replaced
1:84a17b3fad1f 2:8947fca5f715
1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gaaui </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 gaaui
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 Calculates various indece of amino acid usage
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 gaaui calculates amino acid usage indices for proteins (excluding<br />
45 formylmethionine). Calculated indices are as follows,<br />
46 Laa: Length in amino acids<br />
47 ndaa: Number of different amino acids<br />
48 Haau: Entropy of amino acid usage<br />
49 mmw: Mean molecular weight<br />
50 gravy: Mean hydropathic indices of each amino acid<br />
51 aroma: Relative frequency of aromatic amino acids<br />
52 <br />
53 G-language SOAP service is provided by the<br />
54 Institute for Advanced Biosciences, Keio University.<br />
55 The original web service is located at the following URL:<br />
56 <br />
57 http://www.g-language.org/wiki/soap<br />
58 <br />
59 WSDL(RPC/Encoded) file is located at:<br />
60 <br />
61 http://soap.g-language.org/g-language.wsdl<br />
62 <br />
63 Documentation on G-language Genome Analysis Environment methods are<br />
64 provided at the Document Center<br />
65 <br />
66 http://ws.g-language.org/gdoc/<br />
67 <br />
68
69 </p>
70
71 <H2>Usage</H2>
72
73 Here is a sample session with gaaui
74
75 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
76
77 % gaaui refseqn:NC_000913
78 Calculates various indece of amino acid usage
79 AAINDEX entry output file [nc_000913.gaaui]:
80
81 </pre></td></tr></table>
82
83 Go to the <a href="#input">input files</a> for this example<br>
84 Go to the <a href="#output">output files</a> for this example<br><br>
85
86 <h2>Command line arguments</h2>
87
88 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
89 <tr bgcolor="#FFFFCC">
90 <th align="left">Qualifier</th>
91 <th align="left">Type</th>
92 <th align="left">Description</th>
93 <th align="left">Allowed values</th>
94 <th align="left">Default</th>
95 </tr>
96
97 <tr bgcolor="#FFFFCC">
98 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
99 </tr>
100
101 <tr bgcolor="#FFFFCC">
102 <td>[-sequence]<br>(Parameter 1)</td>
103 <td>seqall</td>
104 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
105 <td>Readable sequence(s)</td>
106 <td><b>Required</b></td>
107 </tr>
108
109 <tr bgcolor="#FFFFCC">
110 <td>[-outfile]<br>(Parameter 2)</td>
111 <td>outfile</td>
112 <td>AAINDEX entry output file</td>
113 <td>Output file</td>
114 <td><i>&lt;*&gt;</i>.gaaui</td>
115 </tr>
116
117 <tr bgcolor="#FFFFCC">
118 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
119 </tr>
120
121 <tr>
122 <td colspan=5>(none)</td>
123 </tr>
124
125 <tr bgcolor="#FFFFCC">
126 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
127 </tr>
128
129 <tr bgcolor="#FFFFCC">
130 <td>-[no]accid</td>
131 <td>boolean</td>
132 <td>Include to use sequence accession ID as query</td>
133 <td>Boolean value Yes/No</td>
134 <td>Yes</td>
135 </tr>
136
137 </table>
138
139
140 <h2 id="input">Input file format</h2>
141
142 <p>
143 The database definitions for following commands are available at<br />
144 http://soap.g-language.org/kbws/embossrc<br />
145 <br />
146 gaaui reads one or more nucleotide sequences.<br />
147 <br />
148
149 </p>
150
151 <h2 id="output">Output file format</h2>
152
153 <p>
154 The output from gaaui is to a plain text file.<br />
155 <br />
156 File: nc_000913.gaaui<br />
157 <br />
158 <table width="90%"><tr><td bgcolor="#CCFFCC">
159 Sequence: NC_000913<br />
160 Laa,ndaa,Haau,mmw,gravy,aroma,gene<br />
161 20,8,2.4842,117.48,+0.0150,0.0000,thrL<br />
162 819,20,4.0887,126.65,+0.0328,0.0659,thrA<br />
163 309,20,4.1228,126.35,+0.0181,0.0712,thrB<br />
164 427,20,4.0806,128.00,-0.1014,0.0843,thrC<br />
165 97,18,3.9165,133.54,-1.0268,0.0928,yaaX<br />
166 257,19,4.0733,132.55,-0.4117,0.1089,yaaA<br />
167 475,20,4.0413,126.46,+0.6781,0.1242,yaaJ<br />
168 316,20,4.0395,128.99,-0.2165,0.0728,talB<br />
169 <br />
170 <font color=red>[Part of this file has been deleted for brevity]</font><br />
171 <br />
172 169,20,4.0001,124.90,+0.0231,0.0710,yjjX<br />
173 214,20,3.9937,129.77,-0.3813,0.0374,ytjC<br />
174 288,20,4.1421,132.58,-0.3628,0.1111,rob<br />
175 156,20,4.0627,126.72,-0.0442,0.0705,creA<br />
176 228,20,4.0471,131.94,-0.1408,0.0789,creB<br />
177 473,20,4.0254,128.01,+0.0023,0.0677,creC<br />
178 449,20,4.0871,128.66,+0.2082,0.0980,creD<br />
179 237,20,4.0729,132.54,-0.4970,0.0675,arcA<br />
180 45,15,3.5800,123.27,+0.7533,0.0222,yjjY<br />
181 227,20,4.0283,128.63,-0.0031,0.0573,yjtD<br />
182 </td></tr></table>
183 <br />
184 <br />
185
186 </p>
187
188 <h2>Data files</h2>
189
190 <p>
191 None.
192 </p>
193
194 <h2>Notes</h2>
195
196 <p>
197 None.
198 </p>
199
200 <h2>References</h2>
201
202 <pre>
203 Lobry, JR. and Gautier, C. (1994) Hydrophobicity, expressivity and
204 aromaticity are the major trends of amino-acid usage in 999 Escherichia
205 coli chromosome-encoded genes, Nucleic Acids Res, 22:3174-3180.a
206
207 Zavala A et al. (2002) Trends in codon and amino acid usage in Thermotoga
208 maritima J Mol Evol. 54(5):563-8.
209
210 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
211 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
212 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
213
214 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
215 large-scale analysis of high-throughput omics data, J. Pest Sci.,
216 31, 7.
217
218 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
219 Analysis Environment with REST and SOAP Web Service Interfaces,
220 Nucleic Acids Res., 38, W700-W705.
221
222 </pre>
223
224 <h2>Warnings</h2>
225
226 <p>
227 None.
228 </p>
229
230 <h2>Diagnostic Error Messages</h2>
231
232 <p>
233 None.
234 </p>
235
236 <h2>Exit status</h2>
237
238 <p>
239 It always exits with a status of 0.
240 </p>
241
242 <h2>Known bugs</h2>
243
244 <p>
245 None.
246 </p>
247
248 <h2>See also</h2>
249
250 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
251 <th>Description</th></tr>
252
253 <tr>
254 <td><a href="gaminoinfo.html">gaminoinfo</a></td>
255 <td>Prints out basic amino acid sequence statistics</td>
256 </tr><tr>
257 <td><a href="gcodoncompiler.html">gcodoncompiler</a></td>
258 <td>Calculate various kinds of amino acid and codon usage data</td>
259 </tr>
260
261 </table>
262
263 <h2>Author(s)</h2>
264
265 <pre>
266 Hidetoshi Itaya (celery@g-language.org)
267 Institute for Advanced Biosciences, Keio University
268 252-0882 Japan
269
270 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
271 Institute for Advanced Biosciences, Keio University
272 252-0882 Japan</pre>
273
274 <h2>History</h2>
275
276 2012 - Written by Hidetoshi Itaya
277
278 <h2>Target users</h2>
279
280 This program is intended to be used by everyone and everything, from
281 naive users to embedded scrips.
282
283 <h2>Comments</h2>
284
285 None.
286