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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: ggeneskew </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 ggeneskew
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 gene strand bias of 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 ggeneskew calculates and plots the strand bias of genes (or the GC skew<br />
45 within them). By default, this program visualizes the gene strand preference<br />
46 (1 for direct, -1 for complement strand), but by specifying -base option<br />
47 option, GC/AT/Purine/Keto skews of the coding regions or more specifically<br />
48 in the GC3 (third codon position) with -gctri option can be calculated.<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 ggeneskew
71
72 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
73
74 % ggeneskew refseqn:NC_000913
75 Calculate the gene strand bias of the given genome
76 Program compseq output file (optional) [nc_000913.ggeneskew]:
77
78 </pre></td></tr></table>
79
80 Go to the <a href="#input">input files</a> for this example<br>
81 Go to the <a href="#output">output files</a> for this example<br><br>
82
83 Example 2
84
85 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
86
87 % ggeneskew refseqn:NC_000913 -plot -graph png
88 Calculate the gene strand bias of the given genome
89 Created ggeneskew.1.png
90
91 </pre></td></tr></table>
92
93 Go to the <a href="#input">input files</a> for this example<br>
94 Go to the <a href="#output">output files</a> for this example<br><br>
95
96 <h2>Command line arguments</h2>
97
98 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
99 <tr bgcolor="#FFFFCC">
100 <th align="left">Qualifier</th>
101 <th align="left">Type</th>
102 <th align="left">Description</th>
103 <th align="left">Allowed values</th>
104 <th align="left">Default</th>
105 </tr>
106
107 <tr bgcolor="#FFFFCC">
108 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
109 </tr>
110
111 <tr bgcolor="#FFFFCC">
112 <td>[-sequence]<br>(Parameter 1)</td>
113 <td>seqall</td>
114 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
115 <td>Readable sequence(s)</td>
116 <td><b>Required</b></td>
117 </tr>
118
119 <tr bgcolor="#FFFFCC">
120 <td>-graph</td>
121 <td>xygraph</td>
122 <td>Graph type</td>
123 <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>
124 <td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
125 </tr>
126
127 <tr bgcolor="#FFFFCC">
128 <td>-outfile</td>
129 <td>outfile</td>
130 <td>Program compseq output file (optional)</td>
131 <td>Output file</td>
132 <td><i>&lt;*&gt;</i>.ggeneskew</td>
133 </tr>
134
135 <tr bgcolor="#FFFFCC">
136 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
137 </tr>
138
139 <tr>
140 <td colspan=5>(none)</td>
141 </tr>
142
143 <tr bgcolor="#FFFFCC">
144 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
145 </tr>
146
147 <tr bgcolor="#FFFFCC">
148 <td>-window</td>
149 <td>integer</td>
150 <td>Window size to observe</td>
151 <td>Any integer value</td>
152 <td>10000</td>
153 </tr>
154
155 <tr bgcolor="#FFFFCC">
156 <td>-slide</td>
157 <td>integer</td>
158 <td>Window slide size</td>
159 <td>Any integer value</td>
160 <td>10000</td>
161 </tr>
162
163 <tr bgcolor="#FFFFCC">
164 <td>-cumulative</td>
165 <td>boolean</td>
166 <td>Input 1 to calculate cumulative skew</td>
167 <td>Boolean value Yes/No</td>
168 <td>No</td>
169 </tr>
170
171 <tr bgcolor="#FFFFCC">
172 <td>-base</td>
173 <td>selection</td>
174 <td>Input 'gc', 'at', 'purine', or 'keto' for observing GC/AT/Purine/Keto skews</td>
175 <td>Choose from selection list of values</td>
176 <td>none</td>
177 </tr>
178
179 <tr bgcolor="#FFFFCC">
180 <td>-gctri</td>
181 <td>boolean</td>
182 <td>Include to use only the third codon positions</td>
183 <td>Boolean value Yes/No</td>
184 <td>No</td>
185 </tr>
186
187 <tr bgcolor="#FFFFCC">
188 <td>-[no]accid</td>
189 <td>boolean</td>
190 <td>Include to use sequence accession ID as query</td>
191 <td>Boolean value Yes/No</td>
192 <td>Yes</td>
193 </tr>
194
195 <tr bgcolor="#FFFFCC">
196 <td>-plot</td>
197 <td>toggle</td>
198 <td>Include to plot result</td>
199 <td>Toggle value Yes/No</td>
200 <td>No</td>
201 </tr>
202
203 </table>
204
205
206 <h2 id="input">Input file format</h2>
207
208 <p>
209 The database definitions for following commands are available at<br />
210 http://soap.g-language.org/kbws/embossrc<br />
211 <br />
212 ggeneskew reads one or more nucleotide sequences.<br />
213 <br />
214
215 </p>
216
217 <h2 id="output">Output file format</h2>
218
219 <p>
220 The output from ggeneskew is to a plain text file or the EMBOSS graphics device.<br />
221 <br />
222 File: nc_000913.ggeneskew<br />
223 <br />
224 <table width="90%"><tr><td bgcolor="#CCFFCC">
225 Sequence: NC_000913<br />
226 location,gene None skew<br />
227 190,0.294118<br />
228 337,-0.058914<br />
229 2801,-0.120000<br />
230 3734,-0.070588<br />
231 5234,0.037500<br />
232 5683,0.020725<br />
233 6529,0.032765<br />
234 8238,-0.028226<br />
235 <br />
236 <font color=red>[Part of this file has been deleted for brevity]</font><br />
237 <br />
238 4631820,-0.093407<br />
239 4632464,-0.006479<br />
240 4633544,-0.120690<br />
241 4634030,-0.060367<br />
242 4634719,-0.104167<br />
243 4636201,-0.144560<br />
244 4637613,0.010929<br />
245 4638425,0.200000<br />
246 4638965,-0.081871<br />
247 ,<br />
248 </td></tr></table>
249
250 </p>
251
252 <h2>Data files</h2>
253
254 <p>
255 None.
256 </p>
257
258 <h2>Notes</h2>
259
260 <p>
261 None.
262 </p>
263
264 <h2>References</h2>
265
266 <pre>
267 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
268 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
269 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
270
271 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
272 large-scale analysis of high-throughput omics data, J. Pest Sci.,
273 31, 7.
274
275 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
276 Analysis Environment with REST and SOAP Web Service Interfaces,
277 Nucleic Acids Res., 38, W700-W705.
278
279 </pre>
280
281 <h2>Warnings</h2>
282
283 <p>
284 None.
285 </p>
286
287 <h2>Diagnostic Error Messages</h2>
288
289 <p>
290 None.
291 </p>
292
293 <h2>Exit status</h2>
294
295 <p>
296 It always exits with a status of 0.
297 </p>
298
299 <h2>Known bugs</h2>
300
301 <p>
302 None.
303 </p>
304
305 <h2>See also</h2>
306
307 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
308 <th>Description</th></tr>
309
310 <tr>
311 <td><a href="ggcskew.html">ggcskew</a></td>
312 <td>Calculates the GC skew of the input sequence</td>
313 </tr><tr>
314 <td><a href="ggcwin.html">ggcwin</a></td>
315 <td>Calculates the GC content along the given genome</td>
316 </tr><tr>
317 <td><a href="ggenomicskew.html">ggenomicskew</a></td>
318 <td>Calculates the GC skew in different regions of the given genome</td>
319 </tr>
320
321 </table>
322
323 <h2>Author(s)</h2>
324
325 <pre>
326 Hidetoshi Itaya (celery@g-language.org)
327 Institute for Advanced Biosciences, Keio University
328 252-0882 Japan
329
330 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
331 Institute for Advanced Biosciences, Keio University
332 252-0882 Japan</pre>
333
334 <h2>History</h2>
335
336 2012 - Written by Hidetoshi Itaya
337
338 <h2>Target users</h2>
339
340 This program is intended to be used by everyone and everything, from
341 naive users to embedded scrips.
342
343 <h2>Comments</h2>
344
345 None.
346