Mercurial > repos > ktnyt > gembassy

comparison GEMBASSY-1.0.3/doc/html/gbaserelativeentropy.html @ 2:8947fca5f715 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ktnyt
date Fri, 26 Jun 2015 05:21:44 -0400
parents 84a17b3fad1f
children
comparison
equal deleted inserted replaced
1:84a17b3fad1f 2:8947fca5f715
1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gbaserelativeentropy </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 gbaserelativeentropy
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 Kullback-Leibler divergence (relative entropy)
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 Kullback-Leibler divergence (relative<br />
46 entropy). In realistic conditions, as background nucleotide composition<br />
47 (e.g. G+C content) varies among species. Kullback-Leibler divergence<br />
48 calculates the entropy with reduced background noise.<br />
49 <br />
50 G-language SOAP service is provided by the<br />
51 Institute for Advanced Biosciences, Keio University.<br />
52 The original web service is located at the following URL:<br />
53 <br />
54 http://www.g-language.org/wiki/soap<br />
55 <br />
56 WSDL(RPC/Encoded) file is located at:<br />
57 <br />
58 http://soap.g-language.org/g-language.wsdl<br />
59 <br />
60 Documentation on G-language Genome Analysis Environment methods are<br />
61 provided at the Document Center<br />
62 <br />
63 http://ws.g-language.org/gdoc/<br />
64 <br />
65
66 </p>
67
68 <H2>Usage</H2>
69
70 Here is a sample session with gbaserelativeentropy
71
72 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
73
74 % gbaserelativeentropy refseqn:NC_000913
75 Calculates and graphs the sequence conservation using Kullback-Leibler
76 divergence (relative entropy)
77 Program compseq output file (optional) [nc_000913.gbaserelativeentropy]:
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 % gbaserelativeentropy refseqn:NC_000913 -plot -graph png
89 Calculates and graphs the sequence conservation using Kullback-Leibler
90 divergence (relative entropy)
91 Created gbaserelativeentropy.1.png
92
93 </pre></td></tr></table>
94
95 Go to the <a href="#input">input files</a> for this example<br>
96 Go to the <a href="#output">output files</a> for this example<br><br>
97
98 <h2>Command line arguments</h2>
99
100 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
101 <tr bgcolor="#FFFFCC">
102 <th align="left">Qualifier</th>
103 <th align="left">Type</th>
104 <th align="left">Description</th>
105 <th align="left">Allowed values</th>
106 <th align="left">Default</th>
107 </tr>
108
109 <tr bgcolor="#FFFFCC">
110 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
111 </tr>
112
113 <tr bgcolor="#FFFFCC">
114 <td>[-sequence]<br>(Parameter 1)</td>
115 <td>seqall</td>
116 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
117 <td>Readable sequence(s)</td>
118 <td><b>Required</b></td>
119 </tr>
120
121 <tr bgcolor="#FFFFCC">
122 <td>-graph</td>
123 <td>xygraph</td>
124 <td>Graph type</td>
125 <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>
126 <td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
127 </tr>
128
129 <tr bgcolor="#FFFFCC">
130 <td>-outfile</td>
131 <td>outfile</td>
132 <td>Program compseq output file (optional)</td>
133 <td>Output file</td>
134 <td><i>&lt;*&gt;</i>.gbaserelativeentropy</td>
135 </tr>
136
137 <tr bgcolor="#FFFFCC">
138 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
139 </tr>
140
141 <tr>
142 <td colspan=5>(none)</td>
143 </tr>
144
145 <tr bgcolor="#FFFFCC">
146 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
147 </tr>
148
149 <tr bgcolor="#FFFFCC">
150 <td>-position</td>
151 <td>selection</td>
152 <td>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</td>
153 <td>Choose from selection list of values</td>
154 <td>start</td>
155 </tr>
156
157 <tr bgcolor="#FFFFCC">
158 <td>-patlen</td>
159 <td>integer</td>
160 <td>Length of oligomer to count</td>
161 <td>Any integer value</td>
162 <td>3</td>
163 </tr>
164
165 <tr bgcolor="#FFFFCC">
166 <td>-upstream</td>
167 <td>integer</td>
168 <td>Length upstream of specified position to create PWM</td>
169 <td>Any integer value</td>
170 <td>30</td>
171 </tr>
172
173 <tr bgcolor="#FFFFCC">
174 <td>-downstream</td>
175 <td>integer</td>
176 <td>Length downstream of specified position to create PWM</td>
177 <td>Any integer value</td>
178 <td>30</td>
179 </tr>
180
181 <tr bgcolor="#FFFFCC">
182 <td>-[no]accid</td>
183 <td>boolean</td>
184 <td>Include to use sequence accession ID as query</td>
185 <td>Boolean value Yes/No</td>
186 <td>Yes</td>
187 </tr>
188
189 <tr bgcolor="#FFFFCC">
190 <td>-plot</td>
191 <td>toggle</td>
192 <td>Include to plot result</td>
193 <td>Toggle value Yes/No</td>
194 <td>No</td>
195 </tr>
196
197 </table>
198
199
200 <h2 id="input">Input file format</h2>
201
202 <p>
203 The database definitions for following commands are available at<br />
204 http://soap.g-language.org/kbws/embossrc<br />
205 <br />
206 gbaserelativeentropy reads one or more nucleotide sequences.<br />
207 <br />
208
209 </p>
210
211 <h2 id="output">Output file format</h2>
212
213 <p>
214 The output from gbaserelativeentropy is to a plain text file or the EMBOSS graphics device.<br />
215 <br />
216 File: nc_000913.gbaserelativeentropy<br />
217 <br />
218 <table width="90%"><tr><td bgcolor="#CCFFCC">
219 Sequence: NC_000913<br />
220 -30,-0.46682<br />
221 -29,-0.46265<br />
222 -28,-0.45732<br />
223 -27,-0.45704<br />
224 -26,-0.44692<br />
225 -25,-0.44396<br />
226 -24,-0.43528<br />
227 -23,-0.43419<br />
228 -22,-0.42518<br />
229 <br />
230 <font color=red>[Part of this file has been deleted for brevity]</font><br />
231 <br />
232 21,-0.40010<br />
233 22,-0.41772<br />
234 23,-0.42503<br />
235 24,-0.39675<br />
236 25,-0.43091<br />
237 26,-0.43196<br />
238 27,-0.40576<br />
239 28,-0.43387<br />
240 29,-0.41228<br />
241 30,-0.38869<br />
242 </td></tr></table>
243
244 </p>
245
246 <h2>Data files</h2>
247
248 <p>
249 None.
250 </p>
251
252 <h2>Notes</h2>
253
254 <p>
255 None.
256 </p>
257
258 <h2>References</h2>
259
260 <pre>
261 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
262 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
263 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
264
265 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
266 large-scale analysis of high-throughput omics data, J. Pest Sci.,
267 31, 7.
268
269 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
270 Analysis Environment with REST and SOAP Web Service Interfaces,
271 Nucleic Acids Res., 38, W700-W705.
272
273 </pre>
274
275 <h2>Warnings</h2>
276
277 <p>
278 None.
279 </p>
280
281 <h2>Diagnostic Error Messages</h2>
282
283 <p>
284 None.
285 </p>
286
287 <h2>Exit status</h2>
288
289 <p>
290 It always exits with a status of 0.
291 </p>
292
293 <h2>Known bugs</h2>
294
295 <p>
296 None.
297 </p>
298
299 <h2>See also</h2>
300
301 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
302 <th>Description</th></tr>
303
304 <tr>
305 <td><a href="gbase_entropy.html">gbase_entropy</a></td>
306 <td>Calculates and graphs the sequence conservation using Shanon uncertainty (entropy)</td>
307 </tr></td>
308 </tr><tr>
309 <td><a href="gbase_information_content.html">gbase_information_content</a></td>
310 <td>Calculates and graphs the sequence conservation using information content</td>
311 </tr>
312
313 </table>
314
315 <h2>Author(s)</h2>
316
317 <pre>
318 Hidetoshi Itaya (celery@g-language.org)
319 Institute for Advanced Biosciences, Keio University
320 252-0882 Japan
321
322 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
323 Institute for Advanced Biosciences, Keio University
324 252-0882 Japan</pre>
325
326 <h2>History</h2>
327
328 2012 - Written by Hidetoshi Itaya
329
330 <h2>Target users</h2>
331
332 This program is intended to be used by everyone and everything, from
333 naive users to embedded scrips.
334
335 <h2>Comments</h2>
336
337 None.
338
339 </BODY>
340 </HTML>