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comparison GEMBASSY-1.0.3/doc/html/gb2.html @ 0:8300eb051bea draft

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author ktnyt
date Fri, 26 Jun 2015 05:19:29 -0400
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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gb2 </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 gb2
18 </font></b>
19 </td></tr>
20 </table>
21 <br>&nbsp;
22 <p>
23
24
25 <!--END OF HEADER-->
26
27
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29
30
31
32 <H2> Function </H2>
33 Calculate strand bias of bacterial genome using B2 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 gb2 calculates strand bias of bacterial genome using B2 index,<br />
45 proposed by Lobry and Sueoka(2002). Basic idea of B2 index is to calculate<br />
46 the distance from neutral parity state (0.5, 0.5), when the bias of<br />
47 the coding regions is plotted in a coordinate system with axes representing<br />
48 G/(G+C) and A/(A+T), using the third codon position of genes. This index<br />
49 measures the degree of transcription- and translation-associated effects of<br />
50 bias from Chargaff's second parity rule.<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 gb2
73
74 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
75
76 % gb2 refseqn:NC_000913
77 Calculate strand bias of bacterial genome using B2 index
78 Program compseq output file [nc_000913.gb2]:
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>.gb2</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>-[no]accid</td>
130 <td>boolean</td>
131 <td>Include to use sequence accession ID as query</td>
132 <td>Boolean value Yes/No</td>
133 <td>Yes</td>
134 </tr>
135
136 </table>
137
138
139 <h2 id="input">Input file format</h2>
140
141 <p>
142 The database definitions for following commands are available at<br />
143 http://soap.g-language.org/kbws/embossrc<br />
144 <br />
145 gb2 reads one or more nucleotide sequences.<br />
146 <br />
147
148 </p>
149
150 <h2 id="output">Output file format</h2>
151
152 <p>
153 The output from gb2 is to a plain text file.<br />
154 <br />
155 File: nc_000913.gb2<br />
156 <br />
157 <table width="90%"><tr><td bgcolor="#CCFFCC">
158 Sequence: NC_000913 B2: 0.0919769585775651<br />
159 </td></tr></table>
160 <br />
161
162 </p>
163
164 <h2>Data files</h2>
165
166 <p>
167 None.
168 </p>
169
170 <h2>Notes</h2>
171
172 <p>
173 None.
174 </p>
175
176 <h2>References</h2>
177
178 <pre>
179 Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in
180 bacteria, Genome Biology, 3(10):0058
181
182 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
183 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
184 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
185
186 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
187 large-scale analysis of high-throughput omics data, J. Pest Sci.,
188 31, 7.
189
190 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
191 Analysis Environment with REST and SOAP Web Service Interfaces,
192 Nucleic Acids Res., 38, W700-W705.
193
194 </pre>
195
196 <h2>Warnings</h2>
197
198 <p>
199 None.
200 </p>
201
202 <h2>Diagnostic Error Messages</h2>
203
204 <p>
205 None.
206 </p>
207
208 <h2>Exit status</h2>
209
210 <p>
211 It always exits with a status of 0.
212 </p>
213
214 <h2>Known bugs</h2>
215
216 <p>
217 None.
218 </p>
219
220 <h2>See also</h2>
221
222 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
223 <th>Description</th></tr>
224
225 <tr>
226 <td><a href="gb1.html">gb1</a></td>
227 <td>Calculate strand bias of bacterial genome using B1 index</td>
228 </tr><tr>
229 <td><a href="gdeltagcskew.html">gdeltagcskew</a></td>
230 <td>Calculate strand bias of bacterial genome using delta GC skew</td>
231 </tr><tr>
232 <td><a href="ggcsi.html">ggcsi</a></td>
233 <td>GC Skew Index: an index for strand-specefic mutational bias</td>
234 </tr><tr>
235 <td><a href="gldabias.html">gldabias</a></td>
236 <td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</td>
237 </tr>
238
239 </table>
240
241 <h2>Author(s)</h2>
242
243 <pre>
244 Hidetoshi Itaya (celery@g-language.org)
245 Institute for Advanced Biosciences, Keio University
246 252-0882 Japan
247
248 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
249 Institute for Advanced Biosciences, Keio University
250 252-0882 Japan</pre>
251
252 <h2>History</h2>
253
254 2012 - Written by Hidetoshi Itaya
255
256 <h2>Target users</h2>
257
258 This program is intended to be used by everyone and everything, from
259 naive users to embedded scrips.
260
261 <h2>Comments</h2>
262
263 None.
264
265 </BODY>
266 </HTML>