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

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: ggcsi </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 ggcsi
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 GC Skew Index: an index for strand-specific mutational bias
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 ggcsi calculates the GC Skew Index (GCSI) of the given circular bacterial<br />
45 genome. GCSI quantifies the degree of GC Skew. In other words, this index<br />
46 represents the degree of strand-specific mutational bias in bacterial<br />
47 genomes, caused by replicational selection. <br />
48 GCSI is calculated by the following formula:<br />
49 <br />
50 GCSI = sqrt((SA/6000) * (dist/600))<br />
51 <br />
52 where SA is the spectral amplitude of Fourier power spectrum at 1Hz,<br />
53 and dist is the normalized Euclidean distance between the vertices of <br />
54 cumulative GC skew.<br />
55 <br />
56 GCSI ranges from 0 (no observable skew) to 1 (strong skew), and Archaeal<br />
57 genomes that have multiple replication origins and therefore have no<br />
58 observable skew mostly have GCSI below 0.05. Escherichia coli genome has<br />
59 values around 0.10.<br />
60 <br />
61 Version 1 of GCSI required fixed number of windows (4096), but the new GCSI<br />
62 version 2 (also known as generalized GCSI: gGCSI) is invariant of the number<br />
63 of windows. GCSI version 1 is calculated as an arithmetic mean (as opposed<br />
64 to the geometric mean of gGCSI) of SR (spectral ratio, the signal-to-noise<br />
65 ratio of 1Hz power spectrum) and dist.<br />
66 <br />
67 G-language SOAP service is provided by the<br />
68 Institute for Advanced Biosciences, Keio University.<br />
69 The original web service is located at the following URL:<br />
70 <br />
71 http://www.g-language.org/wiki/soap<br />
72 <br />
73 WSDL(RPC/Encoded) file is located at:<br />
74 <br />
75 http://soap.g-language.org/g-language.wsdl<br />
76 <br />
77 Documentation on G-language Genome Analysis Environment methods are<br />
78 provided at the Document Center<br />
79 <br />
80 http://ws.g-language.org/gdoc/<br />
81 <br />
82
83 </p>
84
85 <H2>Usage</H2>
86
87 Here is a sample session with ggcsi
88
89 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
90
91 % ggcsi refseqn:NC_000913
92 GC Skew Index: an index for strand-specific mutational bias
93 Program compseq output file [nc_000913.ggcsi]:
94
95 </pre></td></tr></table>
96
97 Go to the <a href="#input">input files</a> for this example<br>
98 Go to the <a href="#output">output files</a> for this example<br><br>
99
100 <h2>Command line arguments</h2>
101
102 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
103 <tr bgcolor="#FFFFCC">
104 <th align="left">Qualifier</th>
105 <th align="left">Type</th>
106 <th align="left">Description</th>
107 <th align="left">Allowed values</th>
108 <th align="left">Default</th>
109 </tr>
110
111 <tr bgcolor="#FFFFCC">
112 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
113 </tr>
114
115 <tr bgcolor="#FFFFCC">
116 <td>[-sequence]<br>(Parameter 1)</td>
117 <td>seqall</td>
118 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
119 <td>Readable sequence(s)</td>
120 <td><b>Required</b></td>
121 </tr>
122
123 <tr bgcolor="#FFFFCC">
124 <td>[-outfile]<br>(Parameter 2)</td>
125 <td>outfile</td>
126 <td>Program compseq output file</td>
127 <td>Output file</td>
128 <td><i>&lt;*&gt;</i>.ggcsi</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>-gcsi</td>
145 <td>selection</td>
146 <td>GCSI version to use</td>
147 <td>Choose from selection list of values</td>
148 <td>2</td>
149 </tr>
150
151 <tr bgcolor="#FFFFCC">
152 <td>-window</td>
153 <td>integer</td>
154 <td>Number of windows. Must be a power of 2</td>
155 <td>Any integer value</td>
156 <td>4096</td>
157 </tr>
158
159 <tr bgcolor="#FFFFCC">
160 <td>-purine</td>
161 <td>boolean</td>
162 <td>Use purine skew for calculation</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>Use keto skew for calculation</td>
171 <td>Boolean value Yes/No</td>
172 <td>No</td>
173 </tr>
174
175 <tr bgcolor="#FFFFCC">
176 <td>-at</td>
177 <td>boolean</td>
178 <td>Use AT skew for calculation</td>
179 <td>Boolean value Yes/No</td>
180 <td>No</td>
181 </tr>
182
183 <tr bgcolor="#FFFFCC">
184 <td>-pval</td>
185 <td>boolean</td>
186 <td>Calculate p-value when GCSI version 2 is selected</td>
187 <td>Boolean value Yes/No</td>
188 <td>No</td>
189 </tr>
190
191 <tr bgcolor="#FFFFCC">
192 <td>-[no]accid</td>
193 <td>boolean</td>
194 <td>Include to use sequence accession ID as query</td>
195 <td>Boolean value Yes/No</td>
196 <td>Yes</td>
197 </tr>
198
199 </table>
200
201
202 <h2>Input file format</h2>
203
204 <p id="input">
205 The database definitions for following commands are available at<br />
206 http://soap.g-language.org/kbws/embossrc<br />
207 <br />
208 ggcsi reads one or more nucleotide sequences.<br />
209 <br />
210
211 </p>
212
213 <h2 id="output">Output file format</h2>
214
215 <p>
216 The output from ggcsi is to a plain text file.<br />
217 <br />
218 File: nc_000913.ggcsi<br />
219 <br />
220 <table width="90%"><tr><td bgcolor="#CCFFCC">
221 Sequence: NC_000913 GCSI: 0.0966615833014818 SA: 487.218569030757 DIST: 69.037726<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="gb1.html">gb1</a></td>
286 <td>Calculate strand bias of bacterial genome using B1 index</td>
287 </tr><tr>
288 <td><a href="gb2.html">gb2</a></td>
289 <td>Calculate strand bias of bacterial genome using B2 index</td>
290 </tr><tr>
291 <td><a href="gdeltagcskew.html">gdeltagcskew</a></td>
292 <td>Calculate strand bias of bacterial genome using delta GC skew</td>
293 </tr><tr>
294 <td><a href="gldabias.html">gldabias</a></td>
295 <td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</td>
296 </tr>
297
298 </table>
299
300 <h2>Author(s)</h2>
301
302 <pre>
303 Hidetoshi Itaya (celery@g-language.org)
304 Institute for Advanced Biosciences, Keio University
305 252-0882 Japan
306
307 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
308 Institute for Advanced Biosciences, Keio University
309 252-0882 Japan</pre>
310
311 <h2>History</h2>
312
313 2012 - Written by Hidetoshi Itaya
314
315 <h2>Target users</h2>
316
317 This program is intended to be used by everyone and everything, from
318 naive users to embedded scrips.
319
320 <h2>Comments</h2>
321
322 None.
323
324 </BODY>
325 </HTML>