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

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gcai </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 gcai
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 codon adaptation index for each gene
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 gcai calculates codon adaptation index (CAI) for each gene. CAI is measure<br />
45 a of the relative adaptiveness of the codon usage of a gene towards the<br />
46 codon usage of highly expressed genes, ranging from 0 (no bias) to 1<br />
47 (maximum bias). CAI can be used as a 'universal' measure of codon usage<br />
48 bias as it is correlated with various gene features such as gene expression<br />
49 level, GC content, and GC skew.<br />
50 <br />
51 G-language SOAP service is provided by the<br />
52 Institute for Advanced Biosciences, Keio University.<br />
53 The original web service is located at the following URL:<br />
54 <br />
55 http://www.g-language.org/wiki/soap<br />
56 <br />
57 WSDL(RPC/Encoded) file is located at:<br />
58 <br />
59 http://soap.g-language.org/g-language.wsdl<br />
60 <br />
61 Documentation on G-language Genome Analysis Environment methods are<br />
62 provided at the Document Center<br />
63 <br />
64 http://ws.g-language.org/gdoc/<br />
65 <br />
66
67 </p>
68
69 <H2>Usage</H2>
70
71 Here is a sample session with gcai
72
73 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
74
75 % gcai refseqn:NC_000913
76 Calculate codon adaptation index for each gene
77 Codon usage output file [nc_000913.gcai]:
78
79 </pre></td></tr></table>
80
81 Go to the <a href="#input">input files</a> for this example<br>
82 Go to the <a href="#output">output files</a> for this example<br><br>
83
84 <h2>Command line arguments</h2>
85
86 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
87 <tr bgcolor="#FFFFCC">
88 <th align="left">Qualifier</th>
89 <th align="left">Type</th>
90 <th align="left">Description</th>
91 <th align="left">Allowed values</th>
92 <th align="left">Default</th>
93 </tr>
94
95 <tr bgcolor="#FFFFCC">
96 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
97 </tr>
98
99 <tr bgcolor="#FFFFCC">
100 <td>[-sequence]<br>(Parameter 1)</td>
101 <td>seqall</td>
102 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
103 <td>Readable sequence(s)</td>
104 <td><b>Required</b></td>
105 </tr>
106
107 <tr bgcolor="#FFFFCC">
108 <td>[-outfile]<br>(Parameter 2)</td>
109 <td>outfile</td>
110 <td>Codon usage output file</td>
111 <td>Output file</td>
112 <td><i>&lt;*&gt;</i>.gcai</td>
113 </tr>
114
115 <tr bgcolor="#FFFFCC">
116 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
117 </tr>
118
119 <tr>
120 <td colspan=5>(none)</td>
121 </tr>
122
123 <tr bgcolor="#FFFFCC">
124 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
125 </tr>
126
127 <tr bgcolor="#FFFFCC">
128 <td>-translate</td>
129 <td>boolean</td>
130 <td>Include when translating using standard codon table</td>
131 <td>Boolean value Yes/No</td>
132 <td>No</td>
133 </tr>
134
135 <tr bgcolor="#FFFFCC">
136 <td>-wabsent</td>
137 <td>string</td>
138 <td>W value of codons absent from a reference set to negative when excludes such codons from the calculation</td>
139 <td>Any string</td>
140 <td>-1</td>
141 </tr>
142
143 <tr bgcolor="#FFFFCC">
144 <td>-[no]accid</td>
145 <td>boolean</td>
146 <td>Include to use sequence accession ID as query</td>
147 <td>Boolean value Yes/No</td>
148 <td>Yes</td>
149 </tr>
150
151 </table>
152
153
154 <h2 id="input">Input file format</h2>
155
156 <p>
157 The database definitions for following commands are available at<br />
158 http://soap.g-language.org/kbws/embossrc<br />
159 <br />
160 gcai reads one or more nucleotide sequences.<br />
161 <br />
162
163 </p>
164
165 <h2 id="output">Output file format</h2>
166
167 <p>
168 The output from gcai is to a plain text file.<br />
169 <br />
170 File: nc_000913.gcai<br />
171 <br />
172 <table width="90%"><tr><td bgcolor="#CCFFCC">
173 Sequence: NC_000913<br />
174 cai,gene<br />
175 0.7256,thrL<br />
176 0.4831,thrA<br />
177 0.4719,thrB<br />
178 0.5178,thrC<br />
179 0.4989,yaaX<br />
180 0.4933,yaaA<br />
181 0.4533,yaaJ<br />
182 0.7074,talB<br />
183 <br />
184 <font color=red>[Part of this file has been deleted for brevity]</font><br />
185 <br />
186 0.4681,yjjX<br />
187 0.4797,ytjC<br />
188 0.5350,rob<br />
189 0.4932,creA<br />
190 0.3918,creB<br />
191 0.4170,creC<br />
192 0.4167,creD<br />
193 0.6466,arcA<br />
194 0.4236,yjjY<br />
195 0.3913,yjtD<br />
196 </td></tr></table>
197
198
199 </p>
200
201 <h2>Data files</h2>
202
203 <p>
204 None.
205 </p>
206
207 <h2>Notes</h2>
208
209 <p>
210 None.
211 </p>
212
213 <h2>References</h2>
214
215 <pre>
216 Sharp PM, Li WH. (1987) The codon Adaptation Index--a measure of directional
217 synonymous codon usage bias, and its potential applications.
218 Nucleic Acids Res. 15(3):1281-95.
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="gp2.html">gp2</a></td>
265 <td>Calculate the P2 index of each gene</td>
266 </tr><tr>
267 <td><a href="gphx.html">gphx</a></td>
268 <td>Identify predicted highly expressed gene</td>
269 </tr>
270
271 </table>
272
273 <h2>Author(s)</h2>
274
275 <pre>
276 Hidetoshi Itaya (celery@g-language.org)
277 Institute for Advanced Biosciences, Keio University
278 252-0882 Japan
279
280 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
281 Institute for Advanced Biosciences, Keio University
282 252-0882 Japan</pre>
283
284 <h2>History</h2>
285
286 2012 - Written by Hidetoshi Itaya
287
288 <h2>Target users</h2>
289
290 This program is intended to be used by everyone and everything, from
291 naive users to embedded scrips.
292
293 <h2>Comments</h2>
294
295 None.
296
297 </BODY>
298 </HTML>