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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gdinuc </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 gdinuc
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 Calculates dinucleotide usage
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 gdinuc calculates dinucleotide usage indices for protein-coding sequences<br />
45 (excluding start and stop codons). Dinucleotide usage is computed as the<br />
46 ratio of observed (O) to expected (E) dinucleotide frequencies within the<br />
47 given sequence. Dinucleotides are known to have consistent patterns within<br />
48 the genome (signatures) and tend to have certain periodicities.<br />
49 <br />
50 G-language SOAP service is provided by the<br />
51 Institute for Advanced Biosciences, Keio University.<br />
52 The original web service is located at the following URL:<br />
53 <br />
54 http://www.g-language.org/wiki/soap<br />
55 <br />
56 WSDL(RPC/Encoded) file is located at:<br />
57 <br />
58 http://soap.g-language.org/g-language.wsdl<br />
59 <br />
60 Documentation on G-language Genome Analysis Environment methods are<br />
61 provided at the Document Center<br />
62 <br />
63 http://ws.g-language.org/gdoc/<br />
64 <br />
65
66 </p>
67
68 <H2>Usage</H2>
69
70 Here is a sample session with gdinuc
71
72 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
73
74 % gdinuc refseqn:NC_000913
75 Calculates dinucleotide usage
76 Program compseq output file [nc_000913.gdinuc]:
77
78 </pre></td></tr></table>
79
80 Go to the <a href="#input">input files</a> for this example<br>
81 Go to the <a href="#output">output files</a> for this example<br><br>
82
83 <h2>Command line arguments</h2>
84
85 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
86 <tr bgcolor="#FFFFCC">
87 <th align="left">Qualifier</th>
88 <th align="left">Type</th>
89 <th align="left">Description</th>
90 <th align="left">Allowed values</th>
91 <th align="left">Default</th>
92 </tr>
93
94 <tr bgcolor="#FFFFCC">
95 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
96 </tr>
97
98 <tr bgcolor="#FFFFCC">
99 <td>[-sequence]<br>(Parameter 1)</td>
100 <td>seqall</td>
101 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
102 <td>Readable sequence(s)</td>
103 <td><b>Required</b></td>
104 </tr>
105
106 <tr bgcolor="#FFFFCC">
107 <td>[-outfile]<br>(Parameter 2)</td>
108 <td>outfile</td>
109 <td>Program compseq output file</td>
110 <td>Output file</td>
111 <td><i>&lt;*&gt;</i>.gdinuc</td>
112 </tr>
113
114 <tr bgcolor="#FFFFCC">
115 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
116 </tr>
117
118 <tr>
119 <td colspan=5>(none)</td>
120 </tr>
121
122 <tr bgcolor="#FFFFCC">
123 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
124 </tr>
125
126 <tr bgcolor="#FFFFCC">
127 <td>-translate</td>
128 <td>boolean</td>
129 <td>Include when translates using standard codon table</td>
130 <td>Boolean value Yes/No</td>
131 <td>No</td>
132 </tr>
133
134 <tr bgcolor="#FFFFCC">
135 <td>-position</td>
136 <td>list</td>
137 <td>Codon position or reading frame</td>
138 <td><table><tr><td>all</td> <td><i>(Assess all codon positions)</i></td></tr><tr><td>12</td> <td><i>(Assess the reading frame 1-2)</i></td></tr><tr><td>23</td> <td><i>(Assess the reading frame 2-3)</i></td></tr><tr><td>31</td> <td><i>(Assess the reading frame 3-1)</i></td></tr></table></td>
139 <td>all</td>
140 </tr>
141
142 <tr bgcolor="#FFFFCC">
143 <td>-delkey</td>
144 <td>string</td>
145 <td>Regular expression to delete key (i.e. amino acids and nucleotides)</td>
146 <td>Any string</td>
147 <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td>
148 </tr>
149
150 <tr bgcolor="#FFFFCC">
151 <td>-[no]accid</td>
152 <td>boolean</td>
153 <td>Include to use sequence accession ID as query</td>
154 <td>Boolean value Yes/No</td>
155 <td>Yes</td>
156 </tr>
157
158 </table>
159
160
161 <h2 id="input">Input file format</h2>
162
163 <p>
164 The database definitions for following commands are available at<br />
165 http://soap.g-language.org/kbws/embossrc<br />
166 <br />
167 gdinuc reads one or more nucleotide sequences.<br />
168 <br />
169
170 </p>
171
172 <h2 id="output">Output file format</h2>
173
174 <p>
175 The output from gdinuc is to a plain text file.<br />
176 <br />
177 File: nc_000913.gdinuc<br />
178 <br />
179 Sequence: NC_000913<br />
180 <br />?<table width="90%"><tr><td bgcolor="#CCFFCC">
181 keys,aa,ac,ag,at,ca,cc,cg,ct,ga,gc,gg,gt,ta,tc,tg,tt,gene,<br />
182 All,1.293,0.921,0.720,1.108,1.022,0.868,1.166,0.925,0.958,1.285,0.897,0.867,0.729,0.891,1.228,1.123,<br />
183 </td></tr></table>
184
185 </p>
186
187 <h2>Data files</h2>
188
189 <p>
190 None.
191 </p>
192
193 <h2>Notes</h2>
194
195 <p>
196 None.
197 </p>
198
199 <h2>References</h2>
200
201 <pre>
202 Yew et al. (2004) Base usage and dinucleotide frequency of infectious
203 bursal disease virus, Virus Genes, 28:1,41-53.
204
205 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
206 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
207 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
208
209 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
210 large-scale analysis of high-throughput omics data, J. Pest Sci.,
211 31, 7.
212
213 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
214 Analysis Environment with REST and SOAP Web Service Interfaces,
215 Nucleic Acids Res., 38, W700-W705.
216
217 </pre>
218
219 <h2>Warnings</h2>
220
221 <p>
222 None.
223 </p>
224
225 <h2>Diagnostic Error Messages</h2>
226
227 <p>
228 None.
229 </p>
230
231 <h2>Exit status</h2>
232
233 <p>
234 It always exits with a status of 0.
235 </p>
236
237 <h2>Known bugs</h2>
238
239 <p>
240 None.
241 </p>
242
243 <h2>See also</h2>
244
245 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
246 <th>Description</th></tr>
247
248 <tr>
249 <td><a href="gbui.html">gbui</a></td>
250 <td>Calculates base usage indices for protein-coding sequences</td>
251 </tr>
252
253 </table>
254
255 <h2>Author(s)</h2>
256
257 <pre>
258 Hidetoshi Itaya (celery@g-language.org)
259 Institute for Advanced Biosciences, Keio University
260 252-0882 Japan
261
262 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
263 Institute for Advanced Biosciences, Keio University
264 252-0882 Japan</pre>
265
266 <h2>History</h2>
267
268 2012 - Written by Hidetoshi Itaya
269
270 <h2>Target users</h2>
271
272 This program is intended to be used by everyone and everything, from
273 naive users to embedded scrips.
274
275 <h2>Comments</h2>
276
277 None.
278
279 </BODY>
280 </HTML>