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

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gcbi </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 gcbi
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 the codon bias index (CBI)
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 gcbi calculates the codon bias index (CBI) for each gene af the given<br />
45 genome. CBI is a directional codon bias which measures the usage of<br />
46 optimal codons in a gene. CBI is similar to Fop, basically taking values<br />
47 from0 (no bias) and 1 (maximum bias) and can take negative values<br />
48 depending on the codon usage.<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 gcbi
71
72 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
73
74 % gcbi refseqn:NC_000913
75 Calculates the codon bias index (CBI)
76 Codon usage output file [nc_000913.gcbi]:
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>Codon usage output file</td>
110 <td>Output file</td>
111 <td><i>&lt;*&gt;</i>.gcbi</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 translating 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>-delkey</td>
136 <td>string</td>
137 <td>Regular expression to delete key</td>
138 <td>Any string</td>
139 <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td>
140 </tr>
141
142 <tr bgcolor="#FFFFCC">
143 <td>-[no]accid</td>
144 <td>boolean</td>
145 <td>Include to use sequence accession ID as query</td>
146 <td>Boolean value Yes/No</td>
147 <td>Yes</td>
148 </tr>
149
150 </table>
151
152
153 <h2 id="input">Input file format</h2>
154
155 <p>
156 The database definitions for following commands are available at<br />
157 http://soap.g-language.org/kbws/embossrc<br />
158 <br />
159 gcbi reads one or more nucleotide sequences.<br />
160 <br />
161
162 </p>
163
164 <h2 id="output">Output file format</h2>
165
166 <p>
167 The output from gcbi is to a plain text file.<br />
168 <br />
169 File: nc_000913.gcbi<br />
170 <br />
171 <table width="90%"><tr><td bgcolor="#CCFFCC">
172 Sequence: NC_000913<br />
173 cbi,gene<br />
174 0.8716,thrL<br />
175 0.3441,thrA<br />
176 0.3462,thrB<br />
177 0.4280,thrC<br />
178 0.3868,yaaX<br />
179 0.3908,yaaA<br />
180 0.3521,yaaJ<br />
181 0.5354,talB<br />
182 <br />
183 <font color=red>[Part of this file has been deleted for brevity]</font><br />
184 <br />
185 0.4005,yjjX<br />
186 0.4388,ytjC<br />
187 0.3934,rob<br />
188 0.4645,creA<br />
189 0.4266,creB<br />
190 0.3435,creC<br />
191 0.3796,creD<br />
192 0.4980,arcA<br />
193 0.5412,yjjY<br />
194 0.4018,yjtD<br />
195 </td></tr></table>
196
197 </p>
198
199 <h2>Data files</h2>
200
201 <p>
202 None.
203 </p>
204
205 <h2>Notes</h2>
206
207 <p>
208 None.
209 </p>
210
211 <h2>References</h2>
212
213 <pre>
214 Comeron JM, Aguade M. (1998) An evaluation of measures of synonymous codon
215 usage bias, J Mol Evol, 47(3):268-74.
216
217 Morton BR (1993) Chloroplast DNA codon use: evidence for selection at the
218 psb A locus based on tRNA availability, J.Mol.Evo,. 37:273-280.
219
220 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
221 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
222 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
223
224 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
225 large-scale analysis of high-throughput omics data, J. Pest Sci.,
226 31, 7.
227
228 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
229 Analysis Environment with REST and SOAP Web Service Interfaces,
230 Nucleic Acids Res., 38, W700-W705.
231
232 </pre>
233
234 <h2>Warnings</h2>
235
236 <p>
237 None.
238 </p>
239
240 <h2>Diagnostic Error Messages</h2>
241
242 <p>
243 None.
244 </p>
245
246 <h2>Exit status</h2>
247
248 <p>
249 It always exits with a status of 0.
250 </p>
251
252 <h2>Known bugs</h2>
253
254 <p>
255 None.
256 </p>
257
258 <h2>See also</h2>
259
260 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
261 <th>Description</th></tr>
262
263 <tr>
264 <td><a href="gdeltaenc.html">gdeltaenc</a></td>
265 <td>Calculate the codon usage bias related to translation optimization (delta ENC)</td>
266 </tr><tr>
267 <td><a href="gicdi.html">gicdi</a></td>
268 <td>Calculates the intrinsic codon deviation index (ICDI)</td>
269 </tr><tr>
270 <td><a href="gsvalue.html">gsvalue</a></td>
271 <td>Calculate the strength of selected codon usage bias (S)</td>
272 </tr>
273
274 </table>
275
276 <h2>Author(s)</h2>
277
278 <pre>
279 Hidetoshi Itaya (celery@g-language.org)
280 Institute for Advanced Biosciences, Keio University
281 252-0882 Japan
282
283 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
284 Institute for Advanced Biosciences, Keio University
285 252-0882 Japan</pre>
286
287 <h2>History</h2>
288
289 2012 - Written by Hidetoshi Itaya
290
291 <h2>Target users</h2>
292
293 This program is intended to be used by everyone and everything, from
294 naive users to embedded scrips.
295
296 <h2>Comments</h2>
297
298 None.
299
300 </BODY>
301 </HTML>