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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gwvalue </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 gwvalue
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 the 'relative adaptiveness of each codon' (W)
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 gwvalue calculates the 'relative adaptiveness of each codon' (W value)<br />
45 which is essential in CAI analysis. W value is calculated by setting the<br />
46 best codon to 1 and calculating the proportion of the other codons.<br />
47 <br />
48 G-language SOAP service is provided by the<br />
49 Institute for Advanced Biosciences, Keio University.<br />
50 The original web service is located at the following URL:<br />
51 <br />
52 http://www.g-language.org/wiki/soap<br />
53 <br />
54 WSDL(RPC/Encoded) file is located at:<br />
55 <br />
56 http://soap.g-language.org/g-language.wsdl<br />
57 <br />
58 Documentation on G-language Genome Analysis Environment methods are<br />
59 provided at the Document Center<br />
60 <br />
61 http://ws.g-language.org/gdoc/<br />
62 <br />
63
64 </p>
65
66 <H2>Usage</H2>
67
68 Here is a sample session with gwvalue
69
70 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
71
72 % gwvalue refseqn:NC_000913
73 Calculate the 'relative adaptiveness of each codon' (W)
74 Codon usage output file [nc_000913.gwvalue]:
75
76 </pre></td></tr></table>
77
78 Go to the <a href="#input">input files</a> for this example<br>
79 Go to the <a href="#output">output files</a> for this example<br><br>
80
81 <h2>Command line arguments</h2>
82
83 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
84 <tr bgcolor="#FFFFCC">
85 <th align="left">Qualifier</th>
86 <th align="left">Type</th>
87 <th align="left">Description</th>
88 <th align="left">Allowed values</th>
89 <th align="left">Default</th>
90 </tr>
91
92 <tr bgcolor="#FFFFCC">
93 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
94 </tr>
95
96 <tr bgcolor="#FFFFCC">
97 <td>[-sequence]<br>(Parameter 1)</td>
98 <td>seqall</td>
99 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
100 <td>Readable sequence(s)</td>
101 <td><b>Required</b></td>
102 </tr>
103
104 <tr bgcolor="#FFFFCC">
105 <td>[-outfile]<br>(Parameter 2)</td>
106 <td>outfile</td>
107 <td>Codon usage output file</td>
108 <td>Output file</td>
109 <td><i>&lt;*&gt;</i>.gwvalue</td>
110 </tr>
111
112 <tr bgcolor="#FFFFCC">
113 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
114 </tr>
115
116 <tr>
117 <td colspan=5>(none)</td>
118 </tr>
119
120 <tr bgcolor="#FFFFCC">
121 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
122 </tr>
123
124 <tr bgcolor="#FFFFCC">
125 <td>-include</td>
126 <td>string</td>
127 <td>Regular expression to include genes in a reference set a reference set in several studies are in-built 1: Nakamura and Tabata, 2: Sharp and Li, 3: Sakai et al.</td>
128 <td>Any string</td>
129 <td>ribosomal.*protein</td>
130 </tr>
131
132 <tr bgcolor="#FFFFCC">
133 <td>-exclude</td>
134 <td>string</td>
135 <td>Regular expression to exclude genes from a reference set</td>
136 <td>Any string</td>
137 <td>[Mm]itochondrial</td>
138 </tr>
139
140 <tr bgcolor="#FFFFCC">
141 <td>-[no]accid</td>
142 <td>boolean</td>
143 <td>Include to use sequence accession ID as query</td>
144 <td>Boolean value Yes/No</td>
145 <td>Yes</td>
146 </tr>
147
148 </table>
149
150
151 <h2>Input file format</h2>
152
153 <p>
154 The database definitions for following commands are available at<br />
155 http://soap.g-language.org/kbws/embossrc<br />
156 <br />
157 gwvalue reads one or more nucleotide sequences.<br />
158 <br />
159
160 </p>
161
162 <h2>Output file format</h2>
163
164 <p>
165 The output from gwvalue is to a plain text file.<br />
166 <br />
167 File: nc_000913.gwvalue<br />
168 <br />
169 <table width="90%"><tr><td bgcolor="#CCFFCC">
170 Sequence: NC_000913<br />
171 Reference set of highly expressed genes<br />
172 product<br />
173 30S ribosomal subunit protein S20<br />
174 30S ribosomal subunit protein S2<br />
175 ribosomal protein S12 methylthiotransferase; radical SAM superfamily<br />
176 ribosomal protein S6 modification protein<br />
177 30S ribosomal subunit protein S1<br />
178 ribosomal-protein-S5-alanine N-acetyltransferase<br />
179 50S ribosomal subunit protein L32<br />
180 <br />
181 <font color=red>[Part of this file has been deleted for brevity]</font><br />
182 <br />
183 T,acc,1.0000<br />
184 T,acg,0.2234<br />
185 T,act,0.9734<br />
186 V,gta,0.4960<br />
187 V,gtc,0.2281<br />
188 V,gtg,0.3422<br />
189 V,gtt,1.0000<br />
190 W,tgg,1.0000<br />
191 Y,tac,1.0000<br />
192 Y,tat,0.5310<br />
193 </td></tr></table>
194
195 </p>
196
197 <h2>Data files</h2>
198
199 <p>
200 None.
201 </p>
202
203 <h2>Notes</h2>
204
205 <p>
206 None.
207 </p>
208
209 <h2>References</h2>
210
211 <pre>
212 Sharp PM et al. (2005) Variation in the strength of selected codon usage
213 bias among bacteria, Nucleic Acids Res. 33(4):1141-1153
214
215 Sakai et al. (2001) Correlation between Shine--Dalgarno sequence
216 conservation and codon usage of bacterial genes, J.Mol.Evol. 52:164-170.
217
218 Nakamura and Tabata (1997) Codon-anticodon assignment and detection of
219 codon usage trends in seven microbial genomes, Microb.Comp.Genomics
220 2:299-312.
221
222 Sharp and Li (1987) The codon Adaptation Index--a measure of directional
223 synonymous codon usage bias, and its potential applications, Nucleic
224 Acids Res. 15:1281-1295.
225
226 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
227 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
228 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
229
230 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
231 large-scale analysis of high-throughput omics data, J. Pest Sci.,
232 31, 7.
233
234 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
235 Analysis Environment with REST and SOAP Web Service Interfaces,
236 Nucleic Acids Res., 38, W700-W705.
237
238 </pre>
239
240 <h2>Warnings</h2>
241
242 <p>
243 None.
244 </p>
245
246 <h2>Diagnostic Error Messages</h2>
247
248 <p>
249 None.
250 </p>
251
252 <h2>Exit status</h2>
253
254 <p>
255 It always exits with a status of 0.
256 </p>
257
258 <h2>Known bugs</h2>
259
260 <p>
261 None.
262 </p>
263
264 <h2>See also</h2>
265
266 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
267 <th>Description</th></tr>
268
269 <tr>
270 <td><a href="genc.html">genc</a></td>
271 <td>Calculate the effective number of codons (Nc)</td>
272 </tr><tr>
273 <td><a href="gew.html">gew</a></td>
274 <td>Calculate a measure of synonymous codon usage evenness (Ew)</td>
275 </tr><tr>
276 <td><a href="gfop.html">gfop</a></td>
277 <td>Calculate the frequency of optimal codons (Fop)</td>
278 </tr><tr>
279 <td><a href="gscs.html">gscs</a></td>
280 <td>Calculates the scaled chi-square</td>
281 </tr>
282
283 </table>
284
285 <h2>Author(s)</h2>
286
287 <pre>
288 Hidetoshi Itaya (celery@g-language.org)
289 Institute for Advanced Biosciences, Keio University
290 252-0882 Japan
291
292 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
293 Institute for Advanced Biosciences, Keio University
294 252-0882 Japan</pre>
295
296 <h2>History</h2>
297
298 2012 - Written by Hidetoshi Itaya
299
300 <h2>Target users</h2>
301
302 This program is intended to be used by everyone and everything, from
303 naive users to embedded scrips.
304
305 <h2>Comments</h2>
306
307 None.
308
309 </BODY>
310 </HTML>