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

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gsvalue </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 gsvalue
18 </font></b>
19 </td></tr>
20 </table>
21 <br>&nbsp;
22 <p>
23
24
25 <!--END OF HEADER-->
26
27
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30
31
32 <H2> Function </H2>
33 Calculate the strength of selected codon usage bias (S)
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 gsvalue calculates the strength of selected codon usage bias (S), also<br />
45 known as Sharp's S index. Using four codon pairs that are recognized by the<br />
46 same tRNA anticodon, namely, Phe(UUC and UUU), Ile(AUC and AUU), Tyr(UAC and<br />
47 UAU), and Asn(AAC and AAU), since the former in each of the pairs has<br />
48 stronger Watson-Crick pairing, selection towards the former codon can be<br />
49 observed for highly expressed genes. S index is therefore the weighted<br />
50 average of such bias, giving an over-all value for a genome, indicating its<br />
51 strength of selected codon usage bias. See Sharp et al. (2005) for details.<br />
52 Sharp originally defined 40 genes as the highly expressed gene group, with<br />
53 tufA, tsf, fusA, rplA-rplF, rplI-rplT, rpsB-rpsT. Since the identificaiton<br />
54 of these genes is not convenient for computational automation, by default,<br />
55 this method uses ribosomal proteins as the highly expressed gene group,<br />
56 as used by Viera-silva and Rocha (2010).<br />
57 However, Sharp's gene group can be optionally used with -sharp option.<br />
58 With this option, all of the 40 genes must be named accordingly in the given<br />
59 genome file.<br />
60 <br />
61 G-language SOAP service is provided by the<br />
62 Institute for Advanced Biosciences, Keio University.<br />
63 The original web service is located at the following URL:<br />
64 <br />
65 http://www.g-language.org/wiki/soap<br />
66 <br />
67 WSDL(RPC/Encoded) file is located at:<br />
68 <br />
69 http://soap.g-language.org/g-language.wsdl<br />
70 <br />
71 Documentation on G-language Genome Analysis Environment methods are<br />
72 provided at the Document Center<br />
73 <br />
74 http://ws.g-language.org/gdoc/<br />
75 <br />
76
77 </p>
78
79 <H2>Usage</H2>
80
81 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
82
83 Here is a sample session with gsvalue
84
85 % gsvalue refseqn:NC_000913
86 Calculate the strength of selected codon usage bias (S)
87 Codon usage output file [nc_000913.gsvalue]:
88
89 </pre></td></tr></table>
90
91 Go to the <a href="#input">input files</a> for this example<br>
92 Go to the <a href="#output">output files</a> for this example<br><br>
93
94 <h2>Command line arguments</h2>
95
96 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
97 <tr bgcolor="#FFFFCC">
98 <th align="left">Qualifier</th>
99 <th align="left">Type</th>
100 <th align="left">Description</th>
101 <th align="left">Allowed values</th>
102 <th align="left">Default</th>
103 </tr>
104
105 <tr bgcolor="#FFFFCC">
106 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
107 </tr>
108
109 <tr bgcolor="#FFFFCC">
110 <td>[-sequence]<br>(Parameter 1)</td>
111 <td>seqall</td>
112 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
113 <td>Readable sequence(s)</td>
114 <td><b>Required</b></td>
115 </tr>
116
117 <tr bgcolor="#FFFFCC">
118 <td>[-outfile]<br>(Parameter 2)</td>
119 <td>outfile</td>
120 <td>Codon usage output file</td>
121 <td>Output file</td>
122 <td><i>&lt;*&gt;</i>.gsvalue</td>
123 </tr>
124
125 <tr bgcolor="#FFFFCC">
126 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
127 </tr>
128
129 <tr>
130 <td colspan=5>(none)</td>
131 </tr>
132
133 <tr bgcolor="#FFFFCC">
134 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
135 </tr>
136
137 <tr bgcolor="#FFFFCC">
138 <td>-sharp</td>
139 <td>boolean</td>
140 <td>Include to use the 40 genes used by Sharp instead of ribosomal proteins</td>
141 <td>Boolean value Yes/No</td>
142 <td>No</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 gsvalue 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 gsvalue is to a plain text file.<br />
171 <br />
172 File: nc_000913.gsvalue<br />
173 <br />
174 <table width="90%"><tr><td bgcolor="#CCFFCC">
175 Sequence: NC_000913 S-value: 1.23467100598485<br />
176 </td></tr></table>
177
178 </p>
179
180 <h2>Data files</h2>
181
182 <p>
183 None.
184 </p>
185
186 <h2>Notes</h2>
187
188 <p>
189 None.
190 </p>
191
192 <h2>References</h2>
193
194 <pre>
195 Sharp PM et al. (2005) "Variation in the strength of selected codon usage
196 bias among bacteria", Nucleic Acids Research, 33(4):1141-1153
197
198 Vieira-Silva S and Rocha EPC (2010) "The systemic imprint of growth and its
199 uses in ecological (meta)genomics", PLoS Genetics, 6(1):e1000808
200
201 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
202 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
203 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
204
205 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
206 large-scale analysis of high-throughput omics data, J. Pest Sci.,
207 31, 7.
208
209 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
210 Analysis Environment with REST and SOAP Web Service Interfaces,
211 Nucleic Acids Res., 38, W700-W705.
212
213 </pre>
214
215 <h2>Warnings</h2>
216
217 <p>
218 None.
219 </p>
220
221 <h2>Diagnostic Error Messages</h2>
222
223 <p>
224 None.
225 </p>
226
227 <h2>Exit status</h2>
228
229 <p>
230 It always exits with a status of 0.
231 </p>
232
233 <h2>Known bugs</h2>
234
235 <p>
236 None.
237 </p>
238
239 <h2>See also</h2>
240
241 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
242 <th>Description</th></tr>
243
244 <tr>
245 <td><a href="gcbi.html">gcbi</a></td>
246 <td>Calculates the codon bias index (CBI)</td>
247 </tr><tr>
248 <td><a href="gdeltaenc.html">gdeltaenc</a></td>
249 <td>Calculate the codon usage bias related to translation optimization (delta ENC)</td>
250 </tr><tr>
251 <td><a href="gicdi.html">gicdi</a></td>
252 <td>Calculates the intrinsic codon deviation index (ICDI)</td>
253 </tr>
254
255 </table>
256
257 <h2>Author(s)</h2>
258
259 <pre>
260 Hidetoshi Itaya (celery@g-language.org)
261 Institute for Advanced Biosciences, Keio University
262 252-0882 Japan
263
264 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
265 Institute for Advanced Biosciences, Keio University
266 252-0882 Japan</pre>
267
268 <h2>History</h2>
269
270 2012 - Written by Hidetoshi Itaya
271
272 <h2>Target users</h2>
273
274 This program is intended to be used by everyone and everything, from
275 naive users to embedded scrips.
276
277 <h2>Comments</h2>
278
279 None.
280
281 </BODY>
282 </HTML>