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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gdeltagcskew </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 gdeltagcskew
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 strand bias of bacterial genome using delta GC skew index
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 gdeltagcskew calculates strand bias of bacterial genome using delta GC skew<br />
45 index, first proposed by Rocha et al. (2001), and further extended in 2006.<br />
46 Basic idea of delta GC skew index is to calculate the difference of GC skew<br />
47 in coding regions residing in leading and lagging strands. Rocha et al.<br />
48 (2001) calculates delta GC skew index using the third codon position of<br />
49 genes, and Rocha et al. (2006) modified to only use >fourfold degenerate<br />
50 codons.<br />
51 <br />
52 G-language SOAP service is provided by the<br />
53 Institute for Advanced Biosciences, Keio University.<br />
54 The original web service is located at the following URL:<br />
55 <br />
56 http://www.g-language.org/wiki/soap<br />
57 <br />
58 WSDL(RPC/Encoded) file is located at:<br />
59 <br />
60 http://soap.g-language.org/g-language.wsdl<br />
61 <br />
62 Documentation on G-language Genome Analysis Environment methods are<br />
63 provided at the Document Center<br />
64 <br />
65 http://ws.g-language.org/gdoc/<br />
66 <br />
67
68 </p>
69
70 <H2>Usage</H2>
71
72 Here is a sample session with gdeltagcskew
73
74 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
75
76 % gdeltagcskew refseqn:NC_000913
77 Calculate strand bias of bacterial genome using delta GC skew index
78 Program compseq output file [nc_000913.gdeltagcskew]:
79
80 </pre></td></tr></table>
81
82 Go to the <a href="#input">input files</a> for this example<br>
83 Go to the <a href="#output">output files</a> for this example<br><br>
84
85 <h2>Command line arguments</h2>
86
87 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
88 <tr bgcolor="#FFFFCC">
89 <th align="left">Qualifier</th>
90 <th align="left">Type</th>
91 <th align="left">Description</th>
92 <th align="left">Allowed values</th>
93 <th align="left">Default</th>
94 </tr>
95
96 <tr bgcolor="#FFFFCC">
97 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
98 </tr>
99
100 <tr bgcolor="#FFFFCC">
101 <td>[-sequence]<br>(Parameter 1)</td>
102 <td>seqall</td>
103 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
104 <td>Readable sequence(s)</td>
105 <td><b>Required</b></td>
106 </tr>
107
108 <tr bgcolor="#FFFFCC">
109 <td>[-outfile]<br>(Parameter 2)</td>
110 <td>outfile</td>
111 <td>Program compseq output file</td>
112 <td>Output file</td>
113 <td><i>&lt;*&gt;</i>.gdeltagcskew</td>
114 </tr>
115
116 <tr bgcolor="#FFFFCC">
117 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
118 </tr>
119
120 <tr>
121 <td colspan=5>(none)</td>
122 </tr>
123
124 <tr bgcolor="#FFFFCC">
125 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
126 </tr>
127
128 <tr bgcolor="#FFFFCC">
129 <td>-at</td>
130 <td>boolean</td>
131 <td>Include when observing AT skew instead of GC skew</td>
132 <td>Boolean value Yes/No</td>
133 <td>No</td>
134 </tr>
135
136 <tr bgcolor="#FFFFCC">
137 <td>-purine</td>
138 <td>boolean</td>
139 <td>Include when observing purine (AG/TC) skew</td>
140 <td>Boolean value Yes/No</td>
141 <td>No</td>
142 </tr>
143
144 <tr bgcolor="#FFFFCC">
145 <td>-keto</td>
146 <td>boolean</td>
147 <td>Include when observing keto (TG/AC) skew</td>
148 <td>Boolean value Yes/No</td>
149 <td>No</td>
150 </tr>
151
152 <tr bgcolor="#FFFFCC">
153 <td>-method</td>
154 <td>selection</td>
155 <td>Choose the nucleotides to use 'degenerate', 'gc3', or 'all'</td>
156 <td>Choose from selection list of values</td>
157 <td>degenerate</td>
158 </tr>
159
160 <tr bgcolor="#FFFFCC">
161 <td>-[no]accid</td>
162 <td>boolean</td>
163 <td>Include to use sequence accession ID as query</td>
164 <td>Boolean value Yes/No</td>
165 <td>Yes</td>
166 </tr>
167
168 </table>
169
170
171 <h2 id="input">Input file format</h2>
172
173 <p>
174 The database definitions for following commands are available at<br />
175 http://soap.g-language.org/kbws/embossrc<br />
176 <br />
177 gdeltagcskew reads one or more nucleotide sequences.<br />
178 <br />
179
180 </p>
181
182 <h2 id="output">Output file format</h2>
183
184 <p>
185 The output from gdeltagcskew is to a plain text file.<br />
186 <br />
187 File: nc_000913.gdeltagcskew<br />
188 <br />
189 <table width="90%"><tr><td bgcolor="#CCFFCC">
190 Sequence: NC_000913 DELTA-GCskew -0.108937<br />
191 </td></tr></table>
192
193 </p>
194
195 <h2>Data files</h2>
196
197 <p>
198 None.
199 </p>
200
201 <h2>Notes</h2>
202
203 <p>
204 None.
205 </p>
206
207 <h2>References</h2>
208
209 <pre>
210 Rocha EPC et al. (2001) Ongoing Evolution of Strand Composition in Bacterial
211 Genomes, Molecular Biology and Evolution, 18(9):1789-1799
212
213 Rocha EPC et al. (2006) Similar compositional biases are caused by very
214 different mutational effects, Genome Research, 16:1537-1547
215
216 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
217 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
218 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
219
220 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
221 large-scale analysis of high-throughput omics data, J. Pest Sci.,
222 31, 7.
223
224 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
225 Analysis Environment with REST and SOAP Web Service Interfaces,
226 Nucleic Acids Res., 38, W700-W705.
227
228 </pre>
229
230 <h2>Warnings</h2>
231
232 <p>
233 None.
234 </p>
235
236 <h2>Diagnostic Error Messages</h2>
237
238 <p>
239 None.
240 </p>
241
242 <h2>Exit status</h2>
243
244 <p>
245 It always exits with a status of 0.
246 </p>
247
248 <h2>Known bugs</h2>
249
250 <p>
251 None.
252 </p>
253
254 <h2>See also</h2>
255
256 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
257 <th>Description</th></tr>
258
259 <tr>
260 <td><a href="gb1.html">gb1</a></td>
261 <td>Calculate strand bias of bacterial genome using B1 index</td>
262 </tr><tr>
263 <td><a href="gb2.html">gb2</a></td>
264 <td>Calculate strand bias of bacterial genome using B2 index</td>
265 </tr><tr>
266 <td><a href="ggcsi.html">ggcsi</a></td>
267 <td>GC Skew Index: an index for strand-specefic mutational bias</td>
268 </tr><tr>
269 <td><a href="gldabias.html">glda_bias</a></td>
270 <td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</td>
271 </tr>
272
273 </table>
274
275 <h2>Author(s)</h2>
276
277 <pre>
278 Hidetoshi Itaya (celery@g-language.org)
279 Institute for Advanced Biosciences, Keio University
280 252-0882 Japan
281
282 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
283 Institute for Advanced Biosciences, Keio University
284 252-0882 Japan</pre>
285
286 <h2>History</h2>
287
288 2012 - Written by Hidetoshi Itaya
289
290 <h2>Target users</h2>
291
292 This program is intended to be used by everyone and everything, from
293 naive users to embedded scrips.
294
295 <h2>Comments</h2>
296
297 None.
298
299 </BODY>
300 </HTML>