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date Fri, 26 Jun 2015 05:21:44 -0400
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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gb1 </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 gb1
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 B1 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 gb1 calculates the strand bias of bacterial genome using B1 index,<br />
45 first proposed by Lobry and Sueoka (2002), and further extended by<br />
46 Rocha et al. (2006). Basic idea of B1 index is to calculate the<br />
47 distance between the two strands, when the leading and lagging strands<br />
48 are plotted in a coordinate system with axes representing G/(G+C) and<br />
49 A/(A+T), using the third codon position of genes. This index measures the<br />
50 degree of replication-induced bias from Chargaff's second parity rule.<br />
51 Rocha et al. modified B1 index to only use >fourfold degenerate codons,<br />
52 and to use T/(A+T) in place of A/(A+T).<br />
53 <br />
54 G-language SOAP service is provided by the<br />
55 Institute for Advanced Biosciences, Keio University.<br />
56 The original web service is located at the following URL:<br />
57 <br />
58 http://www.g-language.org/wiki/soap<br />
59 <br />
60 WSDL(RPC/Encoded) file is located at:<br />
61 <br />
62 http://soap.g-language.org/g-language.wsdl<br />
63 <br />
64 Documentation on G-language Genome Analysis Environment methods are<br />
65 provided at the Document Center<br />
66 <br />
67 http://ws.g-language.org/gdoc/<br />
68 <br />
69
70 </p>
71
72 <H2>Usage</H2>
73
74 Here is a sample session with gb1
75
76 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
77
78 % gb1 refseqn:NC_000913
79 Calculate strand bias of bacterial genome using B1 index
80 Program compseq output file [nc_000913.gb1]:
81
82 </pre></td></tr></table>
83
84 Go to the <a href="#input">input files</a> for this example<br>
85 Go to the <a href="#output">output files</a> for this example<br><br>
86
87 <h2>Command line arguments</h2>
88
89 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
90 <tr bgcolor="#FFFFCC">
91 <th align="left">Qualifier</th>
92 <th align="left">Type</th>
93 <th align="left">Description</th>
94 <th align="left">Allowed values</th>
95 <th align="left">Default</th>
96 </tr>
97
98 <tr bgcolor="#FFFFCC">
99 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
100 </tr>
101
102 <tr bgcolor="#FFFFCC">
103 <td>[-sequence]<br>(Parameter 1)</td>
104 <td>seqall</td>
105 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
106 <td>Readable sequence(s)</td>
107 <td><b>Required</b></td>
108 </tr>
109
110 <tr bgcolor="#FFFFCC">
111 <td>[-outfile]<br>(Parameter 2)</td>
112 <td>outfile</td>
113 <td>Program compseq output file</td>
114 <td>Output file</td>
115 <td><i>&lt;*&gt;</i>.gb1</td>
116 </tr>
117
118 <tr bgcolor="#FFFFCC">
119 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
120 </tr>
121
122 <tr>
123 <td colspan=5>(none)</td>
124 </tr>
125
126 <tr bgcolor="#FFFFCC">
127 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
128 </tr>
129
130 <tr bgcolor="#FFFFCC">
131 <td>-method</td>
132 <td>selection</td>
133 <td>Choose method of 'lobry' or 'rocha'</td>
134 <td>Choose from selection list of values</td>
135 <td>rocha</td>
136 </tr>
137
138 <tr bgcolor="#FFFFCC">
139 <td>-[no]accid</td>
140 <td>boolean</td>
141 <td>Include to use sequence accession ID as query</td>
142 <td>Boolean value Yes/No</td>
143 <td>Yes</td>
144 </tr>
145
146 </table>
147
148
149 <h2 id="input">Input file format</h2>
150
151 <p>
152 The database definitions for following commands are available at<br />
153 http://soap.g-language.org/kbws/embossrc<br />
154 <br />
155 gb1 reads one or more nucleotide sequences.<br />
156 <br />
157
158 </p>
159
160 <h2 id="output">Output file format</h2>
161
162 <p>
163 The output from gb1 is to a plain text file.<br />
164 <br />
165 File: nc_000913.gb1<br />
166 <br />
167 <table width="90%"><tr><td bgcolor="#CCFFCC">
168 Sequence: NC_000913 B1: 0.0630702874711314<br />
169 </td></tr></table>
170
171 </p>
172
173 <h2>Data files</h2>
174
175 <p>
176 None.
177 </p>
178
179 <h2>Notes</h2>
180
181 <p>
182 None.
183 </p>
184
185 <h2>References</h2>
186
187 <pre>
188 Lobry JR and Sueoka N (2002) Asymmetric directional mutation pressures in
189 bacteria, Genome Biology, 3(10):0058
190
191 Rocha EPC et al. (2006) Similar compositional biases are caused by very
192 different mutational effects, Genome Research, 16:1537-1547
193
194 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
195 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
196 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
197
198 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
199 large-scale analysis of high-throughput omics data, J. Pest Sci.,
200 31, 7.
201
202 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
203 Analysis Environment with REST and SOAP Web Service Interfaces,
204 Nucleic Acids Res., 38, W700-W705.
205
206 </pre>
207
208 <h2>Warnings</h2>
209
210 <p>
211 None.
212 </p>
213
214 <h2>Diagnostic Error Messages</h2>
215
216 <p>
217 None.
218 </p>
219
220 <h2>Exit status</h2>
221
222 <p>
223 It always exits with a status of 0.
224 </p>
225
226 <h2>Known bugs</h2>
227
228 <p>
229 None.
230 </p>
231
232 <h2>See also</h2>
233
234 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
235 <th>Description</th></tr>
236
237 <tr>
238 <td><a href="gb2.html">gb2</a></td>
239 <td>Calculate strand bias of bacterial genome using B2 index</td>
240 </tr><tr>
241 <td><a href="gdeltagcskew.html">gdeltagcskew</a></td>
242 <td>Calculate strand bias of bacterial genome using delta GC skew</td>
243 </tr><tr>
244 <td><a href="ggcsi.html">ggcsi</a></td>
245 <td>GC Skew Index: an index for strand-specefic mutational bias</td>
246 </tr><tr>
247 <td><a href="gldabias.html">gldabias</a></td>
248 <td>Calculate strand bias of bacterial genome using linear discriminant analysis (LDA)</td>
249 </tr>
250
251 </table>
252
253 <h2>Author(s)</h2>
254
255 <pre>
256 Hidetoshi Itaya (celery@g-language.org)
257 Institute for Advanced Biosciences, Keio University
258 252-0882 Japan
259
260 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
261 Institute for Advanced Biosciences, Keio University
262 252-0882 Japan</pre>
263
264 <h2>History</h2>
265
266 2012 - Written by Hidetoshi Itaya
267
268 <h2>Target users</h2>
269
270 This program is intended to be used by everyone and everything, from
271 naive users to embedded scrips.
272
273 <h2>Comments</h2>
274
275 None.
276