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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gbui </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 gbui
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 Calculates base usage indices for protein-coding sequences
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 gbui calculates base usage indices of protein-coding sequences (excluding<br />
45 start and stop codons) for each gene. Indices calculated are as follows,<br />
46 acgt: Total bumber of bases (A+T+G+C)<br />
47 ryr: Purine/Pyrimidine ratio (A+G)/(T+C)<br />
48 gcc: G+C content (G+C)/(A+T+G+C)<br />
49 Hgc: entropy of G+C content (G+C)/(A+T+G+C)<br />
50 gcs: GC skew (C-G)/(C+G)<br />
51 ats: AT skew (A-T)/(A+T)<br />
52 <br />
53 G-language SOAP service is provided by the<br />
54 Institute for Advanced Biosciences, Keio University.<br />
55 The original web service is located at the following URL:<br />
56 <br />
57 http://www.g-language.org/wiki/soap<br />
58 <br />
59 WSDL(RPC/Encoded) file is located at:<br />
60 <br />
61 http://soap.g-language.org/g-language.wsdl<br />
62 <br />
63 Documentation on G-language Genome Analysis Environment methods are<br />
64 provided at the Document Center<br />
65 <br />
66 http://ws.g-language.org/gdoc/<br />
67 <br />
68
69 </p>
70
71 <H2>Usage</H2>
72
73 Here is a sample session with gbui
74
75 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
76
77 % gbui refseqn:NC_000913
78 Calculates base usage indices for protein-coding sequences
79 Program compseq output file [nc_000913.gbui]:
80
81 </pre></td></tr></table>
82
83 Go to the <a href="#input">input files</a> for this example<br>
84 Go to the <a href="#output">output files</a> for this example<br><br>
85
86 <h2>Command line arguments</h2>
87
88 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
89 <tr bgcolor="#FFFFCC">
90 <th align="left">Qualifier</th>
91 <th align="left">Type</th>
92 <th align="left">Description</th>
93 <th align="left">Allowed values</th>
94 <th align="left">Default</th>
95 </tr>
96
97 <tr bgcolor="#FFFFCC">
98 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
99 </tr>
100
101 <tr bgcolor="#FFFFCC">
102 <td>[-sequence]<br>(Parameter 1)</td>
103 <td>seqall</td>
104 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
105 <td>Readable sequence(s)</td>
106 <td><b>Required</b></td>
107 </tr>
108
109 <tr bgcolor="#FFFFCC">
110 <td>[-outfile]<br>(Parameter 2)</td>
111 <td>outfile</td>
112 <td>Program compseq output file</td>
113 <td>Output file</td>
114 <td><i>&lt;*&gt;</i>.gbui</td>
115 </tr>
116
117 <tr bgcolor="#FFFFCC">
118 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
119 </tr>
120
121 <tr>
122 <td colspan=5>(none)</td>
123 </tr>
124
125 <tr bgcolor="#FFFFCC">
126 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
127 </tr>
128
129 <tr bgcolor="#FFFFCC">
130 <td>-translate</td>
131 <td>boolean</td>
132 <td>Include when translating using standard codon table</td>
133 <td>Boolean value Yes/No</td>
134 <td>No</td>
135 </tr>
136
137 <tr bgcolor="#FFFFCC">
138 <td>-position</td>
139 <td>list</td>
140 <td>Codon position</td>
141 <td><table><tr><td>all</td> <td><i>(Assess overall base usage of the gene)</i></td></tr><tr><td>1</td> <td><i>(Assess base usage at 1st position of codons)</i></td></tr><tr><td>2</td> <td><i>(Assess base usage at 2nd position of codons)</i></td></tr><tr><td>3</td> <td><i>(Assess base usage at 3rd position of codons)</i></td></tr></table></td>
142 <td>all</td>
143 </tr>
144
145 <tr bgcolor="#FFFFCC">
146 <td>-delkey</td>
147 <td>string</td>
148 <td>Regular expression to delete key</td>
149 <td>Any string</td>
150 <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td>
151 </tr>
152
153 <tr bgcolor="#FFFFCC">
154 <td>-[no]accid</td>
155 <td>boolean</td>
156 <td>Include to use sequence accession ID as query</td>
157 <td>Boolean value Yes/No</td>
158 <td>Yes</td>
159 </tr>
160
161 </table>
162
163
164 <h2 id="input">Input file format</h2>
165
166 <p>
167 The database definitions for following commands are available at<br />
168 http://soap.g-language.org/kbws/embossrc<br />
169 <br />
170 gbui reads one or more nucleotide sequences.<br />
171 <br />
172
173 </p>
174
175 <h2 id="output">Output file format</h2>
176
177 <p>
178 The output from gbui is to a plain text file.<br />
179 <br />
180 File: nc_000913.gbui<br />
181 <br />
182 <table width="90%"><tr><td bgcolor="#CCFFCC">
183 Sequence: NC_000913<br />
184 acgt,ryr,gcc,Hgc,gcs,ats,gene<br />
185 60,0.9355,0.5333,0.9968,+0.3750,+0.3571,thrL<br />
186 2457,1.0206,0.5311,0.9972,-0.0575,-0.0434,thrA<br />
187 927,1.0973,0.5653,0.9877,-0.1183,-0.0471,thrB<br />
188 1281,1.0795,0.5301,0.9974,-0.0692,+0.0033,thrC<br />
189 291,1.0638,0.5430,0.9947,+0.0506,+0.1278,yaaX<br />
190 771,1.0615,0.4994,1.0000,-0.0182,+0.0415,yaaA<br />
191 1425,0.8363,0.5347,0.9965,-0.0315,-0.2278,yaaJ<br />
192 948,1.1303,0.5222,0.9986,-0.0263,+0.0993,talB<br />
193 <br />
194 <font color=red>[Part of this file has been deleted for brevity]</font><br />
195 <br />
196 507,1.0444,0.5661,0.9874,-0.1080,-0.0909,yjjX<br />
197 642,1.1472,0.5654,0.9876,-0.0909,+0.0394,ytjC<br />
198 864,0.9636,0.5347,0.9965,+0.0087,-0.0299,rob<br />
199 468,1.1273,0.4936,0.9999,-0.1169,+0.0042,creA<br />
200 684,1.0118,0.5556,0.9911,-0.0579,-0.0592,creB<br />
201 1419,1.0655,0.5398,0.9954,-0.1018,-0.0505,creC<br />
202 1347,1.0660,0.4974,1.0000,-0.1433,-0.0783,creD<br />
203 711,1.0850,0.5134,0.9995,-0.0082,+0.0751,arcA<br />
204 135,0.8493,0.4370,0.9885,+0.2203,+0.0263,yjjY<br />
205 681,1.1415,0.5007,1.0000,-0.0792,+0.0529,yjtD<br />
206 </td></tr></table>
207
208 </p>
209
210 <h2>Data files</h2>
211
212 <p>
213 None.
214 </p>
215
216 <h2>Notes</h2>
217
218 <p>
219 None.
220 </p>
221
222 <h2>References</h2>
223
224 <pre>
225 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
226 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
227 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
228
229 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
230 large-scale analysis of high-throughput omics data, J. Pest Sci.,
231 31, 7.
232
233 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
234 Analysis Environment with REST and SOAP Web Service Interfaces,
235 Nucleic Acids Res., 38, W700-W705.
236
237 </pre>
238
239 <h2>Warnings</h2>
240
241 <p>
242 None.
243 </p>
244
245 <h2>Diagnostic Error Messages</h2>
246
247 <p>
248 None.
249 </p>
250
251 <h2>Exit status</h2>
252
253 <p>
254 It always exits with a status of 0.
255 </p>
256
257 <h2>Known bugs</h2>
258
259 <p>
260 None.
261 </p>
262
263 <h2>See also</h2>
264
265 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
266 <th>Description</th></tr>
267
268 <tr>
269 <td><a href="gdinuc.html">gdinuc</a></td>
270 <td>Calculates dinucleotide usage</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>