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date Fri, 26 Jun 2015 05:21:44 -0400
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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gp2 </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 gp2
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 the P2 index of 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 gp2 calculates the P2 index for each gene. This index describes<br />
45 the proportion of codons conforming to the intermediate strength of<br />
46 codon-anticodon interaction energy rule of Grosjean and Fiers:<br />
47 P2 = (WWC+SSU)/(WWY+SSY) where W = A or U, S = C or G, and Y = C or U.<br />
48 It indicates the efficiency of the codon-anticodon interaction, and has<br />
49 been used as an indicator of the presence of translational selection.<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 gp2
72
73 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
74
75 % gp2 refseqn:NC_000913
76 Calculate the P2 index of each gene
77 Codon usage output file [nc_000913.gp2]:
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>.gp2</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>-[no]accid</td>
129 <td>boolean</td>
130 <td>Include to use sequence accession ID as query</td>
131 <td>Boolean value Yes/No</td>
132 <td>Yes</td>
133 </tr>
134
135 </table>
136
137
138 <h2 id="input">Input file format</h2>
139
140 <p>
141 The database definitions for following commands are available at<br />
142 http://soap.g-language.org/kbws/embossrc<br />
143 <br />
144 gp2 reads one or more nucleotide sequences.<br />
145 <br />
146
147 </p>
148
149 <h2 id="output">Output file format</h2>
150
151 <p>
152 The output from gp2 is to a plain text file.<br />
153 <br />
154 File: nc_000913.gp2<br />
155 <br />
156 <table width="90%"><tr><td bgcolor="#CCFFCC">
157 Sequence: NC_000913<br />
158 P2,gene<br />
159 0.4444,thrL<br />
160 0.4234,thrA<br />
161 0.4565,thrB<br />
162 0.5156,thrC<br />
163 0.4074,yaaX<br />
164 0.4494,yaaA<br />
165 0.3621,yaaJ<br />
166 0.6832,talB<br />
167 <br />
168 <font color=red>[Part of this file has been deleted for brevity]</font><br />
169 <br />
170 0.3692,yjjX<br />
171 0.4912,ytjC<br />
172 0.4271,rob<br />
173 0.4318,creA<br />
174 0.3065,creB<br />
175 0.3851,creC<br />
176 0.4320,creD<br />
177 0.6395,arcA<br />
178 0.7857,yjjY<br />
179 0.3333,yjtD<br />
180 </td></tr></table>
181
182 </p>
183
184 <h2>Data files</h2>
185
186 <p>
187 None.
188 </p>
189
190 <h2>Notes</h2>
191
192 <p>
193 None.
194 </p>
195
196 <h2>References</h2>
197
198 <pre>
199 Gouy M, Gautier C. (1982) Codon usage in bacteria: correlation with gene
200 expressivity, Nucleic Acids Res, 10(22):7055-74.
201
202 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
203 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
204 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
205
206 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
207 large-scale analysis of high-throughput omics data, J. Pest Sci.,
208 31, 7.
209
210 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
211 Analysis Environment with REST and SOAP Web Service Interfaces,
212 Nucleic Acids Res., 38, W700-W705.
213
214 </pre>
215
216 <h2>Warnings</h2>
217
218 <p>
219 None.
220 </p>
221
222 <h2>Diagnostic Error Messages</h2>
223
224 <p>
225 None.
226 </p>
227
228 <h2>Exit status</h2>
229
230 <p>
231 It always exits with a status of 0.
232 </p>
233
234 <h2>Known bugs</h2>
235
236 <p>
237 None.
238 </p>
239
240 <h2>See also</h2>
241
242 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
243 <th>Description</th></tr>
244
245 <tr>
246 <td><a href="gcai.html">gcai</a></td>
247 <td>Calculate codon adaptation index for each gene</td>
248 </tr><tr>
249 <td><a href="gphx.html">gphx</a></td>
250 <td>Identify predicted highly expressed gene</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>