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comparison GEMBASSY-1.0.3/doc/html/gew.html @ 0:8300eb051bea draft

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gew </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 gew
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 Calculate a measure of synonymous codon usage evenness (Ew)
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 gew calculates the 'weighted sum of relative entropy' (Ew) as a measure
45 <br />
46 of synonymous codon usage evenness for each gene. This index takes all
47 <br />
48 three aspects of amino acid usage (number of distinct amino acids,
49 <br />
50 relatieve frequencies, and degree of codon degeneracy) into account.<br />
51 The values range from 0 (no bias) to 1 (maximum bias).<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 gew
74
75 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
76
77 % gew refseqn:NC_000913
78 Calculate a measure of synonymous codon usage evenness (Ew)
79 Codon usage output file [nc_000913.gew]:
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>Codon usage output file</td>
113 <td>Output file</td>
114 <td><i>&lt;*&gt;</i>.gew</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>-translate</td>
131 <td>boolean</td>
132 <td>Include when translates using standard codon table</td>
133 <td>Boolean value Yes/No</td>
134 <td>No</td>
135 </tr>
136
137 <tr bgcolor="#FFFFCC">
138 <td>-delkey</td>
139 <td>string</td>
140 <td>Regular expression to delete key (i.e. amino acids and nucleotides)</td>
141 <td>Any string</td>
142 <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td>
143 </tr>
144
145 <tr bgcolor="#FFFFCC">
146 <td>-[no]accid</td>
147 <td>boolean</td>
148 <td>Include to use sequence accession ID as query</td>
149 <td>Boolean value Yes/No</td>
150 <td>Yes</td>
151 </tr>
152
153 </table>
154
155
156 <h2 id="input">Input file format</h2>
157
158 <p>
159 The database definitions for following commands are available at<br />
160 http://soap.g-language.org/kbws/embossrc<br />
161 <br />
162 gew reads one or more nucleotide sequences.<br />
163 <br />
164
165 </p>
166
167 <h2 id="output">Output file format</h2>
168
169 <p>
170 The output from gew is to a plain text file.<br />
171 <br />
172 File: nc_000913.gew<br />
173 <br />
174 <table width="90%"><tr><td bgcolor="#CCFFCC">
175 Sequence: NC_000913<br />
176 Ew,gene<br />
177 0.2800,thrL<br />
178 0.8458,thrA<br />
179 0.8292,thrB<br />
180 0.7937,thrC<br />
181 0.7032,yaaX<br />
182 0.7922,yaaA<br />
183 0.8100,yaaJ<br />
184 0.6685,talB<br />
185 <br />
186 <font color=red>[Part of this file has been deleted for brevity]</font><br />
187 <br />
188 0.7943,yjjX<br />
189 0.7265,ytjC<br />
190 0.7932,rob<br />
191 0.7498,creA<br />
192 0.7967,creB<br />
193 0.8490,creC<br />
194 0.7979,creD<br />
195 0.6826,arcA<br />
196 0.6475,yjjY<br />
197 0.7729,yjtD<br />
198 </td></tr></table>
199
200 </p>
201
202 <h2>Data files</h2>
203
204 <p>
205 None.
206 </p>
207
208 <h2>Notes</h2>
209
210 <p>
211 None.
212 </p>
213
214 <h2>References</h2>
215
216 <pre>
217 Suzuki H. et al. (2004) The 'weighted sum of relative entropy': a new
218 index for synonymous codon usage bias, Gene, 23;335:19-23.
219
220 Suzuki H. et al. (2007) Variation in the correlation of G + C composition
221 with synonymous codon usage bias among bacteria, EURASIP J Bioinform
222 Syst Biol, 2007:61374.
223
224 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
225 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
226 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
227
228 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
229 large-scale analysis of high-throughput omics data, J. Pest Sci.,
230 31, 7.
231
232 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
233 Analysis Environment with REST and SOAP Web Service Interfaces,
234 Nucleic Acids Res., 38, W700-W705.
235
236 </pre>
237
238 <h2>Warnings</h2>
239
240 <p>
241 None.
242 </p>
243
244 <h2>Diagnostic Error Messages</h2>
245
246 <p>
247 None.
248 </p>
249
250 <h2>Exit status</h2>
251
252 <p>
253 It always exits with a status of 0.
254 </p>
255
256 <h2>Known bugs</h2>
257
258 <p>
259 None.
260 </p>
261
262 <h2>See also</h2>
263
264 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
265 <th>Description</th></tr>
266
267 <tr>
268 <td><a href="genc.html">genc</a></td>
269 <td>Calculate the effective number of codons (Nc)</td>
270 </tr><tr>
271 <td><a href="gfop.html">gfop</a></td>
272 <td>Calculate the frequency of optimal codons (Fop)</td>
273 </tr><tr>
274 <td><a href="gscs.html">gscs</a></td>
275 <td>Calculates the scaled chi-square</td>
276 </tr><tr>
277 <td><a href="gwvalue.html">gwvalue</a></td>
278 <td>Calculate the 'relative adaptiveness of each codon' (W)</td>
279 </tr>
280
281 </table>
282
283 <h2>Author(s)</h2>
284
285 <pre>
286 Hidetoshi Itaya (celery@g-language.org)
287 Institute for Advanced Biosciences, Keio University
288 252-0882 Japan
289
290 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
291 Institute for Advanced Biosciences, Keio University
292 252-0882 Japan</pre>
293
294 <h2>History</h2>
295
296 2012 - Written by Hidetoshi Itaya
297
298 <h2>Target users</h2>
299
300 This program is intended to be used by everyone and everything, from
301 naive users to embedded scrips.
302
303 <h2>Comments</h2>
304
305 None.
306
307 </BODY>
308 </HTML>