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

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: genc </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 genc
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 effective number of codons (Nc)
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 genc calculates the effective number of codons (ENC|Nc). ENC is a measure<br />
45 for species-independent codon usage bias. Some measures including CAI are<br />
46 species-dependent as optimal codons differ. ENC assigns a gene a number<br />
47 between 20 to 61 where 20 indicates that one codon is used for each amino<br />
48 acid and 61 indicates that each codon is used equally throughout the<br />
49 protein sequence.<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 genc
72
73 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
74
75 % genc refseqn:NC_000913
76 Calculate the effective number of codons (Nc)
77 Codon usage output file [nc_000913.genc]:
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>.genc</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>-delkey</td>
137 <td>string</td>
138 <td>Regular expression to delete key (i.e. amino acids and nucleotides)</td>
139 <td>Any string</td>
140 <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td>
141 </tr>
142
143 <tr bgcolor="#FFFFCC">
144 <td>-[no]accid</td>
145 <td>boolean</td>
146 <td>Include to use sequence accession ID as query</td>
147 <td>Boolean value Yes/No</td>
148 <td>Yes</td>
149 </tr>
150
151 </table>
152
153
154 <h2 id="input">Input file format</h2>
155
156 <p>
157 The database definitions for following commands are available at<br />
158 http://soap.g-language.org/kbws/embossrc<br />
159 <br />
160 genc reads one or more nucleotide sequences.<br />
161 <br />
162
163 </p>
164
165 <h2 id="output">Output file format</h2>
166
167 <p>
168 The output from genc is to a plain text file.<br />
169 <br />
170 File: nc_000913.genc<br />
171 <br />
172 <table width="90%"><tr><td bgcolor="#CCFFCC">
173 Sequence: NC_000913<br />
174 enc,gene<br />
175 ,thrL<br />
176 48.41,thrA<br />
177 54.13,thrB<br />
178 46.18,thrC<br />
179 51.65,yaaX<br />
180 45.71,yaaA<br />
181 48.54,yaaJ<br />
182 36.83,talB<br />
183 <br />
184 <font color=red>[Part of this file has been deleted for brevity]</font><br />
185 <br />
186 51.43,yjjX<br />
187 46.61,ytjC<br />
188 49.83,rob<br />
189 47.74,creA<br />
190 50.63,creB<br />
191 51.39,creC<br />
192 48.42,creD<br />
193 41.53,arcA<br />
194 61,yjjY<br />
195 53.63,yjtD<br />
196 </td></tr></table>
197
198 </p>
199
200 <h2>Data files</h2>
201
202 <p>
203 None.
204 </p>
205
206 <h2>Notes</h2>
207
208 <p>
209 None.
210 </p>
211
212 <h2>References</h2>
213
214 <pre>
215 Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
216 usage bias, J Mol Evol, 47(3):268-74.
217
218 Wright F. (1990) The 'effective number of codons' used in a gene, Gene,
219 87:23-29.
220
221 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
222 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
223 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
224
225 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
226 large-scale analysis of high-throughput omics data, J. Pest Sci.,
227 31, 7.
228
229 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
230 Analysis Environment with REST and SOAP Web Service Interfaces,
231 Nucleic Acids Res., 38, W700-W705.
232
233 </pre>
234
235 <h2>Warnings</h2>
236
237 <p>
238 None.
239 </p>
240
241 <h2>Diagnostic Error Messages</h2>
242
243 <p>
244 None.
245 </p>
246
247 <h2>Exit status</h2>
248
249 <p>
250 It always exits with a status of 0.
251 </p>
252
253 <h2>Known bugs</h2>
254
255 <p>
256 None.
257 </p>
258
259 <h2>See also</h2>
260
261 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
262 <th>Description</th></tr>
263
264 <tr>
265 <td><a href="gew.html">gew</a></td>
266 <td>Calculate a measure of synonymous codon usage evenness (Ew)</td>
267 </tr><tr>
268 <td><a href="gfop.html">gfop</a></td>
269 <td>Calculate the frequency of optimal codons (Fop)</td>
270 </tr><tr>
271 <td><a href="gscs.html">gscs</a></td>
272 <td>Calculates the scaled chi-square</td>
273 </tr><tr>
274 <td><a href="gwvalue.html">gwvalue</a></td>
275 <td>Calculate the 'relative adaptiveness of each codon' (W)</td>
276 </tr>
277
278 </table>
279
280 <h2>Author(s)</h2>
281
282 <pre>
283 Hidetoshi Itaya (celery@g-language.org)
284 Institute for Advanced Biosciences, Keio University
285 252-0882 Japan
286
287 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
288 Institute for Advanced Biosciences, Keio University
289 252-0882 Japan</pre>
290
291 <h2>History</h2>
292
293 2012 - Written by Hidetoshi Itaya
294
295 <h2>Target users</h2>
296
297 This program is intended to be used by everyone and everything, from
298 naive users to embedded scrips.
299
300 <h2>Comments</h2>
301
302 None.
303
304 </BODY>
305 </HTML>