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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gbaseinformationcontent </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 gbaseinformationcontent
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 Calculates and graphs the sequence conservation using information content
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 This function calculates and graphs the sequence conservation in regions<br />
45 around the start/stop codons using information content. Values are obtained<br />
46 by subtracting the entropy for each positfion from the maximum possible value<br />
47 (which will be 2 in the case of nucleotide sequences). Information content<br />
48 will show the highest value when the frequency is most biased to a single<br />
49 alphabet.<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 gbaseinformationcontent
72
73 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
74
75 % gbaseinformationcontent refseqn:NC_000913
76 Calculates and graphs the sequence conservation using information content
77 Program compseq output file (optional) [nc_000913.gbaseinformationcontent]:
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 Example 2
85
86 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
87
88 % gbaseinformationcontent refseqn:NC_000913 -plot -graph png
89 Calculates and graphs the sequence conservation using information content
90 Created gbaseinformationcontent.1.png
91
92 </pre></td></tr></table>
93
94 Go to the <a href="#input">input files</a> for this example<br>
95 Go to the <a href="#output">output files</a> for this example<br><br>
96
97 <h2>Command line arguments</h2>
98
99 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
100 <tr bgcolor="#FFFFCC">
101 <th align="left">Qualifier</th>
102 <th align="left">Type</th>
103 <th align="left">Description</th>
104 <th align="left">Allowed values</th>
105 <th align="left">Default</th>
106 </tr>
107
108 <tr bgcolor="#FFFFCC">
109 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
110 </tr>
111
112 <tr bgcolor="#FFFFCC">
113 <td>[-sequence]<br>(Parameter 1)</td>
114 <td>seqall</td>
115 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
116 <td>Readable sequence(s)</td>
117 <td><b>Required</b></td>
118 </tr>
119
120 <tr bgcolor="#FFFFCC">
121 <td>-graph</td>
122 <td>xygraph</td>
123 <td>Graph type</td>
124 <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td>
125 <td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
126 </tr>
127
128 <tr bgcolor="#FFFFCC">
129 <td>-outfile</td>
130 <td>outfile</td>
131 <td>Program compseq output file (optional)</td>
132 <td>Output file</td>
133 <td><i>&lt;*&gt;</i>.gbaseinformationcontent</td>
134 </tr>
135
136 <tr bgcolor="#FFFFCC">
137 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
138 </tr>
139
140 <tr>
141 <td colspan=5>(none)</td>
142 </tr>
143
144 <tr bgcolor="#FFFFCC">
145 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
146 </tr>
147
148 <tr bgcolor="#FFFFCC">
149 <td>-position</td>
150 <td>selection</td>
151 <td>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</td>
152 <td>Choose from selection list of values</td>
153 <td>start</td>
154 </tr>
155
156 <tr bgcolor="#FFFFCC">
157 <td>-upstream</td>
158 <td>integer</td>
159 <td>Length upstream of specified position to create PWM</td>
160 <td>Any integer value</td>
161 <td>30</td>
162 </tr>
163
164 <tr bgcolor="#FFFFCC">
165 <td>-downstream</td>
166 <td>integer</td>
167 <td>Length downstream of specified position to create PWM</td>
168 <td>Any integer value</td>
169 <td>30</td>
170 </tr>
171
172 <tr bgcolor="#FFFFCC">
173 <td>-patlen</td>
174 <td>integer</td>
175 <td>Length of oligomer to count</td>
176 <td>Any integer value</td>
177 <td>3</td>
178 </tr>
179
180 <tr bgcolor="#FFFFCC">
181 <td>-[no]accid</td>
182 <td>boolean</td>
183 <td>Include to use sequence accession ID as query</td>
184 <td>Boolean value Yes/No</td>
185 <td>Yes</td>
186 </tr>
187
188 <tr bgcolor="#FFFFCC">
189 <td>-plot</td>
190 <td>toggle</td>
191 <td>Include to plot result</td>
192 <td>Toggle value Yes/No</td>
193 <td>No</td>
194 </tr>
195
196 </table>
197
198
199 <h2 id="input">Input file format</h2>
200
201 <p>
202 The database definitions for following commands are available at<br />
203 http://soap.g-language.org/kbws/embossrc<br />
204 <br />
205 gbaseinformationcontent reads one or more nucleotide sequences.<br />
206 <br />
207
208 </p>
209
210 <h2 id="output">Output file format</h2>
211
212 <p>
213 The output from gbaseinformationcontent is to a plain text file or the EMBOSS graphics device.<br />
214 <br />
215 File: nc_000913.gbaseinformationcontent<br />
216 <br />
217 <table width="90%"><tr><td bgcolor="#CCFFCC">
218 Sequence: NC_000913<br />
219 -30,2.42457<br />
220 -29,2.42811<br />
221 -28,2.43235<br />
222 -27,2.43116<br />
223 -26,2.44278<br />
224 -25,2.44236<br />
225 -24,2.44502<br />
226 -23,2.46097<br />
227 -22,2.46588<br />
228 <br />
229 <font color=red>[Part of this file has been deleted for brevity]</font><br />
230 <br />
231 21,2.27547<br />
232 22,2.46974<br />
233 23,2.46342<br />
234 24,2.32686<br />
235 25,2.46245<br />
236 26,2.46061<br />
237 27,2.27664<br />
238 28,2.45650<br />
239 29,2.48206<br />
240 30,2.29140<br />
241 </td></tr></table>
242
243 </p>
244
245 <h2>Data files</h2>
246
247 <p>
248 None.
249 </p>
250
251 <h2>Notes</h2>
252
253 <p>
254 None.
255 </p>
256
257 <h2>References</h2>
258
259 <pre>
260 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
261 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
262 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
263
264 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
265 large-scale analysis of high-throughput omics data, J. Pest Sci.,
266 31, 7.
267
268 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
269 Analysis Environment with REST and SOAP Web Service Interfaces,
270 Nucleic Acids Res., 38, W700-W705.
271
272 </pre>
273
274 <h2>Warnings</h2>
275
276 <p>
277 None.
278 </p>
279
280 <h2>Diagnostic Error Messages</h2>
281
282 <p>
283 None.
284 </p>
285
286 <h2>Exit status</h2>
287
288 <p>
289 It always exits with a status of 0.
290 </p>
291
292 <h2>Known bugs</h2>
293
294 <p>
295 None.
296 </p>
297
298 <h2>See also</h2>
299
300 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
301 <th>Description</th></tr>
302
303 <tr>
304 <td><a href="gbaseentropy.html">gbaseentropy</a></td>
305 <td>Calculates and graphs the sequence conservation using Shanon uncertainty (entropy)</td>
306 </tr><tr>
307 <td><a href="gbaserelativeentropy.html">gbaserelativeentropy</a></td>
308 <td>Calculates and graphs the sequence conservation using Kullback-Leibler divergence (relative entropy)</td>
309 </tr>
310
311 </table>
312
313 <h2>Author(s)</h2>
314
315 <pre>
316 Hidetoshi Itaya (celery@g-language.org)
317 Institute for Advanced Biosciences, Keio University
318 252-0882 Japan
319
320 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
321 Institute for Advanced Biosciences, Keio University
322 252-0882 Japan</pre>
323
324 <h2>History</h2>
325
326 2012 - Written by Hidetoshi Itaya
327
328 <h2>Target users</h2>
329
330 This program is intended to be used by everyone and everything, from
331 naive users to embedded scrips.
332
333 <h2>Comments</h2>
334
335 None.
336
337 </BODY>
338 </HTML>