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

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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gdeltaenc </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 gdeltaenc
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 the codon usage bias related to translation optimization (delta ENC)
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 gdeltaenc calculates the codon usage bias related to translation<br />
45 optimization (delta ENC) described in Rocha (2004). The basic idea is to<br />
46 calculate the Effective Number of Codons (ENC) for highly-expressed genes<br />
47 (ribosomal genes) and weakly-expressed genes (all genes), and taking the<br />
48 relative difference between them. ENC assigns a gene a number between 20 to<br />
49 61 where 20 indicates that one codon is used for each aminoacid and 61<br />
50 indicates that each codon is used equally throughout the protein sequence.<br />
51 <br />
52 G-language SOAP service is provided by the<br />
53 Institute for Advanced Biosciences, Keio University.<br />
54 The original web service is located at the following URL:<br />
55 <br />
56 http://www.g-language.org/wiki/soap<br />
57 <br />
58 WSDL(RPC/Encoded) file is located at:<br />
59 <br />
60 http://soap.g-language.org/g-language.wsdl<br />
61 <br />
62 Documentation on G-language Genome Analysis Environment methods are<br />
63 provided at the Document Center<br />
64 <br />
65 http://ws.g-language.org/gdoc/<br />
66 <br />
67
68 </p>
69
70 <H2>Usage</H2>
71
72 Here is a sample session with gdeltaenc
73
74 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
75
76 % gdeltaenc refseqn:NC_000913
77 Calculate the codon usage bias related to translation optimization (delta
78 ENC)
79 Program compseq output file [nc_000913.gdeltaenc]:
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>.gdeltaenc</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>-[no]accid</td>
131 <td>boolean</td>
132 <td>Include to use sequence accession ID as query</td>
133 <td>Boolean value Yes/No</td>
134 <td>Yes</td>
135 </tr>
136
137 </table>
138
139
140 <h2 id="input">Input file format</h2>
141
142 <p>
143 The database definitions for following commands are available at<br />
144 http://soap.g-language.org/kbws/embossrc<br />
145 <br />
146 gdeltaenc reads one or more nucleotide sequences.<br />
147 <br />
148
149 </p>
150
151 <h2 id="output">Output file format</h2>
152
153 <p>
154 The output from gdeltaenc is to a plain text file.<br />
155 <br />
156 File: nc_000913.gdeltaenc<br />
157 <br />
158 <table width="90%"><tr><td bgcolor="#CCFFCC">
159 Sequence: NC_000913 DELTA-ENC 0.255663430420712<br />
160 </td></tr></table>
161
162 </p>
163
164 <h2>Data files</h2>
165
166 <p>
167 None.
168 </p>
169
170 <h2>Notes</h2>
171
172 <p>
173 None.
174 </p>
175
176 <h2>References</h2>
177
178 <pre>
179 Rocha EPC (2004) Codon usage bias from tRNA's point of view: Redundancy,
180 specialization, and efficient decoding for translation optimization,
181 Genome Research, 14(11):2279-2286
182
183 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
184 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
185 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
186
187 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
188 large-scale analysis of high-throughput omics data, J. Pest Sci.,
189 31, 7.
190
191 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
192 Analysis Environment with REST and SOAP Web Service Interfaces,
193 Nucleic Acids Res., 38, W700-W705.
194
195 </pre>
196
197 <h2>Warnings</h2>
198
199 <p>
200 None.
201 </p>
202
203 <h2>Diagnostic Error Messages</h2>
204
205 <p>
206 None.
207 </p>
208
209 <h2>Exit status</h2>
210
211 <p>
212 It always exits with a status of 0.
213 </p>
214
215 <h2>Known bugs</h2>
216
217 <p>
218 None.
219 </p>
220
221 <h2>See also</h2>
222
223 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
224 <th>Description</th></tr>
225
226 <tr>
227 <td><a href="gcbi.html">gcbi</a></td>
228 <td>Calculates the codon bias index (CBI)</td>
229 </tr><tr>
230 <td><a href="gicdi.html">gicdi</a></td>
231 <td>Calculates the intrinsic codon deviation index (ICDI)</td>
232 </tr><tr>
233 <td><a href="gsvalue.html">gsvalue</a></td>
234 <td>Calculate the strength of selected codon usage bias (S)</td>
235 </tr>
236
237 </table>
238
239 <h2>Author(s)</h2>
240
241 <pre>
242 Hidetoshi Itaya (celery@g-language.org)
243 Institute for Advanced Biosciences, Keio University
244 252-0882 Japan
245
246 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
247 Institute for Advanced Biosciences, Keio University
248 252-0882 Japan</pre>
249
250 <h2>History</h2>
251
252 2012 - Written by Hidetoshi Itaya
253
254 <h2>Target users</h2>
255
256 This program is intended to be used by everyone and everything, from
257 naive users to embedded scrips.
258
259 <h2>Comments</h2>
260
261 None.
262
263 </BODY>
264 </HTML>