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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gldabias </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 gldabias
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 linear discriminant
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 gldabias calculates strand bias of bacterial genome using linear<br />
45 discriminant analysis (LDA), as proposed in Reference 1. The basic idea is<br />
46 to use composition data of genes to train and predict the strand of genes<br />
47 residing either on the leading or the lagging strand. For computational<br />
48 efficiency, this method trans and predicts the strands at putative<br />
49 replication origin as reported by the rep_ori_ter() method. This usually<br />
50 results in maximum predictability of LDA within bacterial genomes.<br />
51 Data to use for LDA can be chosen from "base", "codonbase", "codon", and<br />
52 "amino", with -variable option.<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 gldabias
75
76 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
77
78 % gldabias refseqn:NC_000913
79 Calculate strand bias of bacterial genome using linear discriminant
80 analysis (LDA)
81 Program compseq output file [nc_000913.gldabias]:
82
83 </pre></td></tr></table>
84
85 Go to the <a href="#input">input files</a> for this example<br>
86 Go to the <a href="#output">output files</a> for this example<br><br>
87
88 <h2>Command line arguments</h2>
89
90 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
91 <tr bgcolor="#FFFFCC">
92 <th align="left">Qualifier</th>
93 <th align="left">Type</th>
94 <th align="left">Description</th>
95 <th align="left">Allowed values</th>
96 <th align="left">Default</th>
97 </tr>
98
99 <tr bgcolor="#FFFFCC">
100 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
101 </tr>
102
103 <tr bgcolor="#FFFFCC">
104 <td>[-sequence]<br>(Parameter 1)</td>
105 <td>seqall</td>
106 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
107 <td>Readable sequence(s)</td>
108 <td><b>Required</b></td>
109 </tr>
110
111 <tr bgcolor="#FFFFCC">
112 <td>[-outfile]<br>(Parameter 2)</td>
113 <td>outfile</td>
114 <td>Program compseq output file</td>
115 <td>Output file</td>
116 <td><i>&lt;*&gt;</i>.gldabias</td>
117 </tr>
118
119 <tr bgcolor="#FFFFCC">
120 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
121 </tr>
122
123 <tr>
124 <td colspan=5>(none)</td>
125 </tr>
126
127 <tr bgcolor="#FFFFCC">
128 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
129 </tr>
130
131 <tr bgcolor="#FFFFCC">
132 <td>-coefficients</td>
133 <td>integer</td>
134 <td>Show LDA coefficients</td>
135 <td>Any integer value</td>
136 <td>0</td>
137 </tr>
138
139 <tr bgcolor="#FFFFCC">
140 <td>-variable</td>
141 <td>selection</td>
142 <td>Data to use for LDA. Either 'base', 'codonbase', 'codon', or 'amino'</td>
143 <td>Choose from selection list of values</td>
144 <td>codon</td>
145 </tr>
146
147 <tr bgcolor="#FFFFCC">
148 <td>-[no]accid</td>
149 <td>boolean</td>
150 <td>Include to use sequence accession ID as query</td>
151 <td>Boolean value Yes/No</td>
152 <td>Yes</td>
153 </tr>
154
155 </table>
156
157
158 <h2 id="input">Input file format</h2>
159
160 <p>
161 The database definitions for following commands are available at<br />
162 http://soap.g-language.org/kbws/embossrc<br />
163 <br />
164 gldabias reads one or more nucleotide sequences.<br />
165 <br />
166
167 </p>
168
169 <h2 id="output">Output file format</h2>
170
171 <p>
172 The output from gldabias is to a plain text file.<br />
173 <br />
174 File: nc_000913.gldabias<br />
175 <br />
176 <table width="90%"><tr><td bgcolor="#CCFFCC">
177 Sequence: NC_000913 LDA-BIAS: 0.742533<br />
178 </td></tr></table>
179
180 </p>
181
182 <h2>Data files</h2>
183
184 <p>
185 None.
186 </p>
187
188 <h2>Notes</h2>
189
190 <p>
191 None.
192 </p>
193
194 <h2>References</h2>
195
196 <pre>
197 Rocha EPC et al. (1999) "Universal replication biases in bacteria",
198 Molecular Microbiology, 32(1):11-16
199
200 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
201 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
202 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
203
204 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
205 large-scale analysis of high-throughput omics data, J. Pest Sci.,
206 31, 7.
207
208 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
209 Analysis Environment with REST and SOAP Web Service Interfaces,
210 Nucleic Acids Res., 38, W700-W705.
211
212 </pre>
213
214 <h2>Warnings</h2>
215
216 <p>
217 None.
218 </p>
219
220 <h2>Diagnostic Error Messages</h2>
221
222 <p>
223 None.
224 </p>
225
226 <h2>Exit status</h2>
227
228 <p>
229 It always exits with a status of 0.
230 </p>
231
232 <h2>Known bugs</h2>
233
234 <p>
235 None.
236 </p>
237
238 <h2>See also</h2>
239
240 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
241 <th>Description</th></tr>
242
243 <tr>
244 <td><a href="gb1.html">gb1</a></td>
245 <td>Calculate strand bias of bacterial genome using B1 index</td>
246 </tr><tr>
247 <td><a href="gb2.html">gb2</a></td>
248 <td>Calculate strand bias of bacterial genome using B2 index</td>
249 </tr><tr>
250 <td><a href="gdeltagcskew.html">gdeltagcskew</a></td>
251 <td>Calculate strand bias of bacterial genome using delta GC skew</td>
252 </tr><tr>
253 <td><a href="ggcsi.html">ggcsi</a></td>
254 <td>GC Skew Index: an index for strand-specefic mutational bias</td>
255 </tr>
256
257 </table>
258
259 <h2>Author(s)</h2>
260
261 <pre>
262 Hidetoshi Itaya (celery@g-language.org)
263 Institute for Advanced Biosciences, Keio University
264 252-0882 Japan
265
266 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
267 Institute for Advanced Biosciences, Keio University
268 252-0882 Japan</pre>
269
270 <h2>History</h2>
271
272 2012 - Written by Hidetoshi Itaya
273
274 <h2>Target users</h2>
275
276 This program is intended to be used by everyone and everything, from
277 naive users to embedded scrips.
278
279 <h2>Comments</h2>
280
281 None.
282
283 </BODY>
284 </HTML>