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date Fri, 26 Jun 2015 05:21:44 -0400
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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gviewcds </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 gviewcds
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 Displays a graph of nucleotide contents around start and stop codons
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 gviewcds creates a graph showing the average A,T,G,C contents<br />
45 around start/stop codons. This is useful to view consensus around<br />
46 start/stop codons and to find characteristic pattern in CDS.<br />
47 <br />
48 G-language SOAP service is provided by the<br />
49 Institute for Advanced Biosciences, Keio University.<br />
50 The original web service is located at the following URL:<br />
51 <br />
52 http://www.g-language.org/wiki/soap<br />
53 <br />
54 WSDL(RPC/Encoded) file is located at:<br />
55 <br />
56 http://soap.g-language.org/g-language.wsdl<br />
57 <br />
58 Documentation on G-language Genome Analysis Environment methods are<br />
59 provided at the Document Center<br />
60 <br />
61 http://ws.g-language.org/gdoc/<br />
62 <br />
63
64 </p>
65
66 <H2>Usage</H2>
67
68 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
69
70 Here is a sample session with gviewcds
71
72 % gviewcds refseqn:NC_000913
73 Displays a graph of nucleotide contents around start and stop codons
74 Program compseq output file (optional) [nc_000913.gviewcds]:
75
76 </pre></td></tr></table>
77
78 Go to the <a href="#input">input files</a> for this example<br>
79 Go to the <a href="#output">output files</a> for this example<br><br>
80
81 Example 2
82
83 <table width="90%"><tr><td bgcolor="#CCFFCC">
84
85 % gviewcds refseqn:NC_000913 -plot -graph png
86 Displays a graph of nucleotide contents around start and stop codons
87 Created gviewcds.1.png
88
89 </pre></td></tr></table>
90
91 Go to the <a href="#input">input files</a> for this example<br>
92 Go to the <a href="#output">output files</a> for this example<br><br>
93
94
95
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>.gviewcds</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>-length</td>
150 <td>integer</td>
151 <td>Length in bases to show around start/stop codons</td>
152 <td>Any integer value</td>
153 <td>100</td>
154 </tr>
155
156 <tr bgcolor="#FFFFCC">
157 <td>-gap</td>
158 <td>integer</td>
159 <td>Gap shown in graph in between start/stop codon neighbors</td>
160 <td>Any integer value</td>
161 <td>3</td>
162 </tr>
163
164 <tr bgcolor="#FFFFCC">
165 <td>-[no]accid</td>
166 <td>boolean</td>
167 <td>Include to use sequence accession ID as query</td>
168 <td>Boolean value Yes/No</td>
169 <td>Yes</td>
170 </tr>
171
172 <tr bgcolor="#FFFFCC">
173 <td>-plot</td>
174 <td>toggle</td>
175 <td>Include to plot result</td>
176 <td>Toggle value Yes/No</td>
177 <td>No</td>
178 </tr>
179
180 </table>
181
182
183 <h2 id="input">Input file format</h2>
184
185 <p>
186 The database definitions for following commands are available at<br />
187 http://soap.g-language.org/kbws/embossrc<br />
188 <br />
189 gviewcds reads one or more nucleotide sequences.<br />
190 <br />
191
192 </p>
193
194 <h2 id="output">Output file format</h2>
195
196 <p>
197 The output from gviewcds is to a plain text file or the EMBOSS graphics device.<br />
198 <br />
199 File: nc_000913.gviewcds<br />
200 <br />
201 <table width="90%"><tr><td bgcolor="#CCFFCC">
202 Sequence: NC_000913<br />
203 position,A,T,G,C<br />
204 1,28.20,27.60,22.18,22.02<br />
205 2,26.05,26.81,23.06,24.08<br />
206 3,27.34,27.37,23.94,21.35<br />
207 4,26.28,28.83,23.01,21.88<br />
208 5,26.72,28.22,22.18,22.88<br />
209 6,26.42,26.72,24.96,21.90<br />
210 7,27.21,28.66,21.95,22.18<br />
211 8,25.47,28.39,23.06,23.08<br />
212 <br />
213 <font color=red>[Part of this file has been deleted for brevity]</font><br />
214 <br />
215 400,26.60,27.44,22.67,23.27<br />
216 401,24.38,26.63,25.05,23.92<br />
217 402,25.03,26.37,23.71,24.87<br />
218 403,25.96,27.53,22.53,23.96<br />
219 404,26.63,25.52,24.17,23.66<br />
220 405,25.68,26.26,23.50,24.54<br />
221 406,24.94,26.86,23.92,24.26<br />
222 407,25.54,26.28,23.73,24.43<br />
223 408,25.28,26.93,24.38,23.39<br />
224 409,26.63,26.46,22.32,24.57<br />
225 </td></tr></table>
226
227 </p>
228
229 <h2>Data files</h2>
230
231 <p>
232 None.
233 </p>
234
235 <h2>Notes</h2>
236
237 <p>
238 None.
239 </p>
240
241 <h2>References</h2>
242
243 <pre>
244 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
245 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
246 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
247
248 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
249 large-scale analysis of high-throughput omics data, J. Pest Sci.,
250 31, 7.
251
252 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
253 Analysis Environment with REST and SOAP Web Service Interfaces,
254 Nucleic Acids Res., 38, W700-W705.
255
256 </pre>
257
258 <h2>Warnings</h2>
259
260 <p>
261 None.
262 </p>
263
264 <h2>Diagnostic Error Messages</h2>
265
266 <p>
267 None.
268 </p>
269
270 <h2>Exit status</h2>
271
272 <p>
273 It always exits with a status of 0.
274 </p>
275
276 <h2>Known bugs</h2>
277
278 <p>
279 None.
280 </p>
281
282 <h2>See also</h2>
283
284 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
285 <th>Description</th></tr>
286
287 <tr>
288 <td><a href="gbasecounter.html">gbasecounter</a></td>
289 <td>Creates a position weight matrix of oligomers around start codon</td>
290 </tr><tr>
291 <td><a href="gbasezvalue.html">gbasezvalue</a></td>
292 <td>Extracts conserved oligomers per position using Z-score</td>
293 </tr>
294
295 </table>
296
297 <h2>Author(s)</h2>
298
299 <pre>
300 Hidetoshi Itaya (celery@g-language.org)
301 Institute for Advanced Biosciences, Keio University
302 252-0882 Japan
303
304 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
305 Institute for Advanced Biosciences, Keio University
306 252-0882 Japan</pre>
307
308 <h2>History</h2>
309
310 2012 - Written by Hidetoshi Itaya
311
312 <h2>Target users</h2>
313
314 This program is intended to be used by everyone and everything, from
315 naive users to embedded scrips.
316
317 <h2>Comments</h2>
318
319 None.
320
321 </BODY>
322 </HTML>