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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: ggenomicskew </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 ggenomicskew
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 skew in different regions 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 ggenomicskew calculates and plots the GC skew for the whole genome, coding<br />
45 regions, intergenic regions, and the third codon. This program is useful in<br />
46 visualizing various base composition bias within the genome. AT skew can be<br />
47 calculated instead of GC skew by toggling the -at qualifier.<br />
48 <br />
49 G-language SOAP service is provided by the<br />
50 Institute for Advanced Biosciences, Keio University.<br />
51 The original web service is located at the following URL:<br />
52 <br />
53 http://www.g-language.org/wiki/soap<br />
54 <br />
55 WSDL(RPC/Encoded) file is located at:<br />
56 <br />
57 http://soap.g-language.org/g-language.wsdl<br />
58 <br />
59 Documentation on G-language Genome Analysis Environment methods are<br />
60 provided at the Document Center<br />
61 <br />
62 http://ws.g-language.org/gdoc/<br />
63 <br />
64
65 </p>
66
67 <H2>Usage</H2>
68
69 Here is a sample session with ggenomicskew
70
71 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
72
73 % ggenomicskew refseqn:NC_000913
74 Calculates the GC skew in different regions of the given genome
75 Program compseq output file (optional) [nc_000913.ggenomicskew]:
76
77 </pre></td></tr></table>?
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="#CCFFFF"><pre>
84
85 % ggenomicskew refseqn:NC_000913 -plot -graph png
86 Calculates the GC skew in different regions of the given genome
87 Created ggenomicskew.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 <h2>Command line arguments</h2>
95
96 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
97 <tr bgcolor="#FFFFCC">
98 <th align="left">Qualifier</th>
99 <th align="left">Type</th>
100 <th align="left">Description</th>
101 <th align="left">Allowed values</th>
102 <th align="left">Default</th>
103 </tr>
104
105 <tr bgcolor="#FFFFCC">
106 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
107 </tr>
108
109 <tr bgcolor="#FFFFCC">
110 <td>[-sequence]<br>(Parameter 1)</td>
111 <td>seqall</td>
112 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
113 <td>Readable sequence(s)</td>
114 <td><b>Required</b></td>
115 </tr>
116
117 <tr bgcolor="#FFFFCC">
118 <td>-graph</td>
119 <td>xygraph</td>
120 <td>Graph type</td>
121 <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>
122 <td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
123 </tr>
124
125 <tr bgcolor="#FFFFCC">
126 <td>-outfile</td>
127 <td>outfile</td>
128 <td>Program compseq output file (optional)</td>
129 <td>Output file</td>
130 <td><i>&lt;*&gt;</i>.ggenomicskew</td>
131 </tr>
132
133 <tr bgcolor="#FFFFCC">
134 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
135 </tr>
136
137 <tr>
138 <td colspan=5>(none)</td>
139 </tr>
140
141 <tr bgcolor="#FFFFCC">
142 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
143 </tr>
144
145 <tr bgcolor="#FFFFCC">
146 <td>-divide</td>
147 <td>integer</td>
148 <td>Window to divide into</td>
149 <td>Any integer value</td>
150 <td>250</td>
151 </tr>
152
153 <tr bgcolor="#FFFFCC">
154 <td>-at</td>
155 <td>boolean</td>
156 <td>Input 1 when observing AT skew instead of GC skew</td>
157 <td>Boolean value Yes/No</td>
158 <td>No</td>
159 </tr>
160
161 <tr bgcolor="#FFFFCC">
162 <td>-[no]accid</td>
163 <td>boolean</td>
164 <td>Include to use sequence accession ID as query</td>
165 <td>Boolean value Yes/No</td>
166 <td>Yes</td>
167 </tr>
168
169 <tr bgcolor="#FFFFCC">
170 <td>-plot</td>
171 <td>toggle</td>
172 <td>Include to plot result</td>
173 <td>Toggle value Yes/No</td>
174 <td>No</td>
175 </tr>
176
177 </table>
178
179
180 <h2 id="input">Input file format</h2>
181
182 <p>
183 The database definitions for following commands are available at<br />
184 http://soap.g-language.org/kbws/embossrc<br />
185 <br />
186 ggenomicskew reads one or more nucleotide sequences.<br />
187 <br />
188
189 </p>
190
191 <h2 id="output">Output file format</h2>
192
193 <p>
194 The output from ggenomicskew is to a plain text file or the EMBOSS graphics device.<br />
195 <br />
196 File: nc_000913.ggenomicskew<br />
197 <br />
198 <table width="90%"><tr><td bgcolor="#CCFFCC">
199 Sequence: NC_000913<br />
200 location,GC skew,coding,intergenic,third codon<br />
201 0,-0.036259,-0.040085,-0.034707,-0.141888,<br />
202 1,-0.031167,-0.035657,0.047953,-0.175758,<br />
203 2,-0.028670,-0.031139,-0.049143,-0.018466,<br />
204 3,-0.016647,-0.004656,-0.102616,0.086181,<br />
205 4,-0.041985,-0.029846,-0.088670,0.015291,<br />
206 5,-0.097093,-0.103813,-0.067275,-0.247401,<br />
207 6,-0.028028,-0.016363,-0.048806,-0.047332,<br />
208 7,-0.055805,-0.059329,-0.020071,-0.123271,<br />
209 <br />
210 <font color=red>[Part of this file has been deleted for brevity]</font><br />
211 <br />
212 241,0.000772,-0.012151,-0.063786,0.069585,<br />
213 242,-0.025787,-0.000384,-0.049143,0.029431,<br />
214 243,0.010516,0.008217,-0.030600,0.128657,<br />
215 244,-0.037115,-0.015134,0.017500,0.035398,<br />
216 245,-0.000317,0.006021,-0.047170,0.091549,<br />
217 246,-0.025417,-0.015190,-0.116608,0.044619,<br />
218 247,-0.038404,-0.035676,-0.135714,0.015375,<br />
219 248,-0.026246,-0.024240,-0.037190,-0.130118,<br />
220 249,-0.053371,-0.057225,-0.022472,-0.082167,<br />
221 250,-0.026316,0.166667,-0.151515,0.000000,<br />
222 </td></tr></table>
223
224 </p>
225
226 <h2>Data files</h2>
227
228 <p>
229 None.
230 </p>
231
232 <h2>Notes</h2>
233
234 <p>
235 None.
236 </p>
237
238 <h2>References</h2>
239
240 <pre>
241 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
242 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
243 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
244
245 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
246 large-scale analysis of high-throughput omics data, J. Pest Sci.,
247 31, 7.
248
249 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
250 Analysis Environment with REST and SOAP Web Service Interfaces,
251 Nucleic Acids Res., 38, W700-W705.
252
253 </pre>
254
255 <h2>Warnings</h2>
256
257 <p>
258 None.
259 </p>
260
261 <h2>Diagnostic Error Messages</h2>
262
263 <p>
264 None.
265 </p>
266
267 <h2>Exit status</h2>
268
269 <p>
270 It always exits with a status of 0.
271 </p>
272
273 <h2>Known bugs</h2>
274
275 <p>
276 None.
277 </p>
278
279 <h2>See also</h2>
280
281 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
282 <th>Description</th></tr>
283
284 <tr>
285 <td><a href="ggcskew.html">ggcskew</a></td>
286 <td>Calculates the GC skew of the input sequence</td>
287 </tr><tr>
288 <td><a href="ggcwin.html">ggcwin</a></td>
289 <td>Calculates the GC content along the given genome</td>
290 </tr><tr>
291 <td><a href="ggeneskew.html">ggeneskew</a></td>
292 <td>Calculate the gene strand bias of the given genome</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>