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

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gfop </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 gfop
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 frequency of optimal codons (Fop)
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 gfop calculates the frequency of optimal codons (Fop).Fop is an index to
45 <br />
46 show the optimization level of synonymous codon usage choice. It is<br />
47 basically a ratio of optimal codons against all codons used. The value<br />
48 of Fop ranges from 0 (no optimal codons are used) and 1 (only optimal<br />
49 codons are used).<br />
50 <br />
51 G-language SOAP service is provided by the<br />
52 Institute for Advanced Biosciences, Keio University.<br />
53 The original web service is located at the following URL:<br />
54 <br />
55 http://www.g-language.org/wiki/soap<br />
56 <br />
57 WSDL(RPC/Encoded) file is located at:<br />
58 <br />
59 http://soap.g-language.org/g-language.wsdl<br />
60 <br />
61 Documentation on G-language Genome Analysis Environment methods are<br />
62 provided at the Document Center<br />
63 <br />
64 http://ws.g-language.org/gdoc/<br />
65 <br />
66
67 </p>
68
69 <H2>Usage</H2>
70
71 Here is a sample session with gfop
72
73 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
74
75 % gfop refseqn:NC_000913
76 Calculate the frequency of optimal codons (Fop)
77 Codon usage output file [nc_000913.gfop]:
78
79 </pre></td></tr></table>
80
81 Go to the <a href="#input">input files</a> for this example<br>
82 Go to the <a href="#output">output files</a> for this example<br><br>
83
84 <h2>Command line arguments</h2>
85
86 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
87 <tr bgcolor="#FFFFCC">
88 <th align="left">Qualifier</th>
89 <th align="left">Type</th>
90 <th align="left">Description</th>
91 <th align="left">Allowed values</th>
92 <th align="left">Default</th>
93 </tr>
94
95 <tr bgcolor="#FFFFCC">
96 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
97 </tr>
98
99 <tr bgcolor="#FFFFCC">
100 <td>[-sequence]<br>(Parameter 1)</td>
101 <td>seqall</td>
102 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
103 <td>Readable sequence(s)</td>
104 <td><b>Required</b></td>
105 </tr>
106
107 <tr bgcolor="#FFFFCC">
108 <td>[-outfile]<br>(Parameter 2)</td>
109 <td>outfile</td>
110 <td>Codon usage output file</td>
111 <td>Output file</td>
112 <td><i>&lt;*&gt;</i>.gfop</td>
113 </tr>
114
115 <tr bgcolor="#FFFFCC">
116 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
117 </tr>
118
119 <tr>
120 <td colspan=5>(none)</td>
121 </tr>
122
123 <tr bgcolor="#FFFFCC">
124 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
125 </tr>
126
127 <tr bgcolor="#FFFFCC">
128 <td>-translate</td>
129 <td>boolean</td>
130 <td>Include when translates using standard codon table</td>
131 <td>Boolean value Yes/No</td>
132 <td>No</td>
133 </tr>
134
135 <tr bgcolor="#FFFFCC">
136 <td>-[no]accid</td>
137 <td>boolean</td>
138 <td>Include to use sequence accession ID as query</td>
139 <td>Boolean value Yes/No</td>
140 <td>Yes</td>
141 </tr>
142
143 </table>
144
145
146 <h2 id="input">Input file format</h2>
147
148 <p>
149 The database definitions for following commands are available at<br />
150 http://soap.g-language.org/kbws/embossrc<br />
151 <br />
152 gfop reads one or more nucleotide sequences.<br />
153 <br />
154
155 </p>
156
157 <h2 id="output">Output file format</h2>
158
159 <p>
160 The output from gfop is to a plain text file.<br />
161 <br />
162 File: nc_000913.gfop<br />
163 <br />
164 <table width="90%"><tr><td bgcolor="#CCFFCC">
165 Sequence: NC_000913<br />
166 Laa,Lc,fop,gene<br />
167 20,5,0.4000,thrL<br />
168 819,133,0.4361,thrA<br />
169 309,46,0.4783,thrB<br />
170 427,69,0.5217,thrC<br />
171 97,7,0.2857,yaaX<br />
172 257,56,0.4643,yaaA<br />
173 475,96,0.3958,yaaJ<br />
174 316,56,0.6964,talB<br />
175 <br />
176 <font color=red>[Part of this file has been deleted for brevity]</font><br />
177 <br />
178 169,27,0.2593,yjjX<br />
179 214,23,0.5652,ytjC<br />
180 288,49,0.4082,rob<br />
181 156,23,0.3478,creA<br />
182 228,26,0.3462,creB<br />
183 473,69,0.3478,creC<br />
184 449,70,0.3286,creD<br />
185 237,46,0.6957,arcA<br />
186 45,10,0.7000,yjjY<br />
187 227,24,0.2500,yjtD<br />
188 </td></tr></table>
189
190 </p>
191
192 <h2>Data files</h2>
193
194 <p>
195 None.
196 </p>
197
198 <h2>Notes</h2>
199
200 <p>
201 None.
202 </p>
203
204 <h2>References</h2>
205
206 <pre>
207 Ikemura, T. (1981) Correlation between the abundance of Escherichia coli
208 transfer RNAs and the occurrence of the respective codons in its protein
209 genes: a proposal for a synonymous codon choice that is optimal for the
210 E. coli translational system, J.Mol.Biol, 151:389-409.
211
212 Ikemura (1985) Codon usage and tRNA content in unicellular and multicellular
213 organisms, Mol.Biol.Evol, 2(1):13-34.
214
215 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
216 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
217 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
218
219 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
220 large-scale analysis of high-throughput omics data, J. Pest Sci.,
221 31, 7.
222
223 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
224 Analysis Environment with REST and SOAP Web Service Interfaces,
225 Nucleic Acids Res., 38, W700-W705.
226
227 </pre>
228
229 <h2>Warnings</h2>
230
231 <p>
232 None.
233 </p>
234
235 <h2>Diagnostic Error Messages</h2>
236
237 <p>
238 None.
239 </p>
240
241 <h2>Exit status</h2>
242
243 <p>
244 It always exits with a status of 0.
245 </p>
246
247 <h2>Known bugs</h2>
248
249 <p>
250 None.
251 </p>
252
253 <h2>See also</h2>
254
255 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
256 <th>Description</th></tr>
257
258 <tr>
259 <td><a href="genc.html">genc</a></td>
260 <td>Calculate the effective number of codons (Nc)</td>
261 </tr><tr>
262 <td><a href="gew.html">gew</a></td>
263 <td>Calculate a measure of synonymous codon usage evenness (Ew)</td>
264 </tr><tr>
265 <td><a href="gscs.html">gscs</a></td>
266 <td>Calculates the scaled chi-square</td>
267 </tr><tr>
268 <td><a href="gwvalue.html">gwvalue</a></td>
269 <td>Calculate the 'relative adaptiveness of each codon' (W)</td>
270 </tr>
271
272 </table>
273
274 <h2>Author(s)</h2>
275
276 <pre>
277 Hidetoshi Itaya (celery@g-language.org)
278 Institute for Advanced Biosciences, Keio University
279 252-0882 Japan
280
281 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
282 Institute for Advanced Biosciences, Keio University
283 252-0882 Japan</pre>
284
285 <h2>History</h2>
286
287 2012 - Written by Hidetoshi Itaya
288
289 <h2>Target users</h2>
290
291 This program is intended to be used by everyone and everything, from
292 naive users to embedded scrips.
293
294 <h2>Comments</h2>
295
296 None.
297
298 </BODY>
299 </HTML>