Mercurial > repos > ktnyt > gembassy

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

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Initial upload
author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
parents
children
comparison
equal deleted inserted replaced
-1:000000000000 0:8300eb051bea
1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: ggcwin </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 ggcwin
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 the GC content along the given genome
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 ggcwin calculates and plots the GC content of the given sequence.<br />
45 <br />
46 G-language SOAP service is provided by the<br />
47 Institute for Advanced Biosciences, Keio University.<br />
48 The original web service is located at the following URL:<br />
49 <br />
50 http://www.g-language.org/wiki/soap<br />
51 <br />
52 WSDL(RPC/Encoded) file is located at:<br />
53 <br />
54 http://soap.g-language.org/g-language.wsdl<br />
55 <br />
56 Documentation on G-language Genome Analysis Environment methods are<br />
57 provided at the Document Center<br />
58 <br />
59 http://ws.g-language.org/gdoc/<br />
60 <br />
61
62 </p>
63
64 <H2>Usage</H2>
65
66 Here is a sample session with ggcwin
67
68 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
69
70 % ggcwin refseqn:NC_000913
71 Calculates the GC content along the given genome
72 Program compseq output file (optional) [nc_000913.ggcwin]:
73
74 </pre></td></tr></table>
75
76 Go to the <a href="#input">input files</a> for this example<br>
77 Go to the <a href="#output">output files</a> for this example<br><br>
78
79 Example 2
80
81 <table width="90%"><tr><td bgcolor="#CCFFCC">
82
83 % ggcwin refseqn:NC_000913 -plot -graph png
84 Calculates the GC content along the given genome
85 Created ggcwin.1.png
86
87 </pre></td></tr></table>
88
89 Go to the <a href="#input">input files</a> for this example<br>
90 Go to the <a href="#output">output files</a> for this example<br><br>
91
92 <h2>Command line arguments</h2>
93
94 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
95 <tr bgcolor="#FFFFCC">
96 <th align="left">Qualifier</th>
97 <th align="left">Type</th>
98 <th align="left">Description</th>
99 <th align="left">Allowed values</th>
100 <th align="left">Default</th>
101 </tr>
102
103 <tr bgcolor="#FFFFCC">
104 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
105 </tr>
106
107 <tr bgcolor="#FFFFCC">
108 <td>[-sequence]<br>(Parameter 1)</td>
109 <td>seqall</td>
110 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
111 <td>Readable sequence(s)</td>
112 <td><b>Required</b></td>
113 </tr>
114
115 <tr bgcolor="#FFFFCC">
116 <td>-graph</td>
117 <td>xygraph</td>
118 <td>Graph type</td>
119 <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>
120 <td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
121 </tr>
122
123 <tr bgcolor="#FFFFCC">
124 <td>-outfile</td>
125 <td>outfile</td>
126 <td>Program compseq output file (optional)</td>
127 <td>Output file</td>
128 <td><i>&lt;*&gt;</i>.ggcwin</td>
129 </tr>
130
131 <tr bgcolor="#FFFFCC">
132 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
133 </tr>
134
135 <tr>
136 <td colspan=5>(none)</td>
137 </tr>
138
139 <tr bgcolor="#FFFFCC">
140 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
141 </tr>
142
143 <tr bgcolor="#FFFFCC">
144 <td>-window</td>
145 <td>integer</td>
146 <td>Window size to observe</td>
147 <td>Any integer value</td>
148 <td>10000</td>
149 </tr>
150
151 <tr bgcolor="#FFFFCC">
152 <td>-at</td>
153 <td>boolean</td>
154 <td>Include for observing AT skew instead of GC skew</td>
155 <td>Boolean value Yes/No</td>
156 <td>No</td>
157 </tr>
158
159 <tr bgcolor="#FFFFCC">
160 <td>-purine</td>
161 <td>boolean</td>
162 <td>Include for observing purine (AG/TC) skew</td>
163 <td>Boolean value Yes/No</td>
164 <td>No</td>
165 </tr>
166
167 <tr bgcolor="#FFFFCC">
168 <td>-keto</td>
169 <td>boolean</td>
170 <td>Include for observing keto (TG/AC) skew default: "0</td>
171 <td>Boolean value Yes/No</td>
172 <td>No</td>
173 </tr>
174
175 <tr bgcolor="#FFFFCC">
176 <td>-plot</td>
177 <td>toggle</td>
178 <td>Include to plot result</td>
179 <td>Toggle value Yes/No</td>
180 <td>No</td>
181 </tr>
182
183 </table>
184
185
186 <h2 id="input">Input file format</h2>
187
188 <p>
189 The database definitions for following commands are available at<br />
190 http://soap.g-language.org/kbws/embossrc<br />
191 <br />
192 ggcwin reads one or more nucleotide sequences.<br />
193 <br />
194
195 </p>
196
197 <h2 id="output">Output file format</h2>
198
199 <p>
200 The output from ggcwin is to a plain text file or the EMBOSS graphics device.<br />
201 <br />
202 File: nc_000913.ggcwin<br />
203 <br />
204 <table width="90%"><tr><td bgcolor="#CCFFCC">
205 Sequence: NC_000913<br />
206 location,GC content<br />
207 0,0.520700<br />
208 10000,0.499400<br />
209 20000,0.526200<br />
210 30000,0.532300<br />
211 40000,0.527700<br />
212 50000,0.515600<br />
213 60000,0.555800<br />
214 70000,0.536000<br />
215 <br />
216 <font color=red>[Part of this file has been deleted for brevity]</font><br />
217 <br />
218 4530000,0.442800<br />
219 4540000,0.487000<br />
220 4550000,0.507700<br />
221 4560000,0.509600<br />
222 4570000,0.444600<br />
223 4580000,0.531600<br />
224 4590000,0.512300<br />
225 4600000,0.504500<br />
226 4610000,0.535600<br />
227 4620000,0.546600<br />
228 </td></tr></table>
229
230 </p>
231
232 <h2>Data files</h2>
233
234 <p>
235 None.
236 </p>
237
238 <h2>Notes</h2>
239
240 <p>
241 None.
242 </p>
243
244 <h2>References</h2>
245
246 <pre>
247 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
248 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
249 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
250
251 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
252 large-scale analysis of high-throughput omics data, J. Pest Sci.,
253 31, 7.
254
255 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
256 Analysis Environment with REST and SOAP Web Service Interfaces,
257 Nucleic Acids Res., 38, W700-W705.
258
259 </pre>
260
261 <h2>Warnings</h2>
262
263 <p>
264 None.
265 </p>
266
267 <h2>Diagnostic Error Messages</h2>
268
269 <p>
270 None.
271 </p>
272
273 <h2>Exit status</h2>
274
275 <p>
276 It always exits with a status of 0.
277 </p>
278
279 <h2>Known bugs</h2>
280
281 <p>
282 None.
283 </p>
284
285 <h2>See also</h2>
286
287 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
288 <th>Description</th></tr>
289
290 <tr>
291 <td><a href="ggcskew.html">ggcskew</a></td>
292 <td>Calculates the GC skew of the input sequence</td>
293 </tr><tr>
294 <td><a href="ggeneskew.html">ggeneskew</a></td>
295 <td>Calculate the gene strand bias of the given genome</td>
296 </tr><tr>
297 <td><a href="ggenomicskew.html">ggenomicskew</a></td>
298 <td>Calculates the GC skew in different regions of the given genome</td>
299 </tr>
300
301 </table>
302
303 <h2>Author(s)</h2>
304
305 <pre>
306 Hidetoshi Itaya (celery@g-language.org)
307 Institute for Advanced Biosciences, Keio University
308 252-0882 Japan
309
310 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
311 Institute for Advanced Biosciences, Keio University
312 252-0882 Japan</pre>
313
314 <h2>History</h2>
315
316 2012 - Written by Hidetoshi Itaya
317
318 <h2>Target users</h2>
319
320 This program is intended to be used by everyone and everything, from
321 naive users to embedded scrips.
322
323 <h2>Comments</h2>
324
325 None.
326