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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gphx </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 gphx
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 Identify predicted highly expressed 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 gphx calculates codon usage differences between gene classes for identifying<br />
45 Predicted Highly eXpressed (PHX) and Putative Alien (PA) genes. A gene is<br />
46 identified as PHX if BgC/BgH >= 1, where BgC and BgH is a value < 1 by it's<br />
47 nature. PHX genes are known to generally have favorable codon usage, strong<br />
48 SD sequences, and probably stronger conservation of promoter sequences.<br />
49 A gene is idenfitied as PA if BgC and BgH is greater than the median of<br />
50 BgC for every gene with a length close to the gene.<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 gphx
73
74 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
75
76 % gphx refseqn:NC_000913
77 Identify predicted highly expressed gene
78 Codon usage output file [nc_000913.gphx]:
79
80 </pre></td></tr></table>
81
82 Go to the <a href="#input">input files</a> for this example<br>
83 Go to the <a href="#output">output files</a> for this example<br><br>
84
85 <h2>Command line arguments</h2>
86
87 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
88 <tr bgcolor="#FFFFCC">
89 <th align="left">Qualifier</th>
90 <th align="left">Type</th>
91 <th align="left">Description</th>
92 <th align="left">Allowed values</th>
93 <th align="left">Default</th>
94 </tr>
95
96 <tr bgcolor="#FFFFCC">
97 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
98 </tr>
99
100 <tr bgcolor="#FFFFCC">
101 <td>[-sequence]<br>(Parameter 1)</td>
102 <td>seqall</td>
103 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
104 <td>Readable sequence(s)</td>
105 <td><b>Required</b></td>
106 </tr>
107
108 <tr bgcolor="#FFFFCC">
109 <td>[-outfile]<br>(Parameter 2)</td>
110 <td>outfile</td>
111 <td>Codon usage output file</td>
112 <td>Output file</td>
113 <td><i>&lt;*&gt;</i>.gphx</td>
114 </tr>
115
116 <tr bgcolor="#FFFFCC">
117 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
118 </tr>
119
120 <tr>
121 <td colspan=5>(none)</td>
122 </tr>
123
124 <tr bgcolor="#FFFFCC">
125 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
126 </tr>
127
128 <tr bgcolor="#FFFFCC">
129 <td>-translate</td>
130 <td>boolean</td>
131 <td>Include when translating using standard codon table</td>
132 <td>Boolean value Yes/No</td>
133 <td>No</td>
134 </tr>
135
136 <tr bgcolor="#FFFFCC">
137 <td>-delkey</td>
138 <td>string</td>
139 <td>Regular expression to delete key</td>
140 <td>Any string</td>
141 <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td>
142 </tr>
143
144 <tr bgcolor="#FFFFCC">
145 <td>-[no]accid</td>
146 <td>boolean</td>
147 <td>Include to use sequence accession ID as query</td>
148 <td>Boolean value Yes/No</td>
149 <td>Yes</td>
150 </tr>
151
152 </table>
153
154
155 <h2 id="input">Input file format</h2>
156
157 <p>
158 The database definitions for following commands are available at<br />
159 http://soap.g-language.org/kbws/embossrc<br />
160 <br />
161 gphx reads one or more nucleotide sequences.<br />
162 <br />
163
164 </p>
165
166 <h2 id="output">Output file format</h2>
167
168 <p>
169 The output from gphx is to a plain text file.<br />
170 <br />
171 File: nc_000913.gphx<br />
172 <br />
173 <table width="90%"><tr><td bgcolor="#CCFFCC">
174 Sequence: NC_000913<br />
175 BgC,BgH,E_g,phx,pa,gene<br />
176 0.8070,0.8977,0.8990,0,1,thrL<br />
177 0.1857,0.5958,0.3116,0,0,thrA<br />
178 0.2323,0.5964,0.3896,0,0,thrB<br />
179 0.2353,0.6064,0.3881,0,0,thrC<br />
180 0.4353,0.6020,0.7231,0,1,yaaX<br />
181 0.2961,0.6790,0.4361,0,0,yaaA<br />
182 0.2233,0.7009,0.3186,0,0,yaaJ<br />
183 0.4149,0.3071,1.3511,1,0,talB<br />
184 <br />
185 [Part of this file has been deleted for brevity]<br />
186 <br />
187 0.3255,0.7038,0.4625,0,0,yjjX<br />
188 0.3531,0.5906,0.5979,0,0,ytjC<br />
189 0.2257,0.5235,0.4311,0,0,rob<br />
190 0.3584,0.6809,0.5264,0,0,creA<br />
191 0.3455,0.7950,0.4346,0,0,creB<br />
192 0.2298,0.7154,0.3212,0,0,creC<br />
193 0.3299,0.7916,0.4167,0,0,creD<br />
194 0.3543,0.3786,0.9357,0,0,arcA<br />
195 0.7295,0.8286,0.8804,0,1,yjjY<br />
196 0.4028,0.8401,0.4795,0,0,yjtD<br />
197 </td></tr></table>
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 CMBL- PHX/PA user guide http://www.cmbl.uga.edu/software/PHX-PA-guide.htm
217
218 Henry I., Sharp PM. (2007) Predicting gene expression level from codon
219 usage bias Mol Biol Evol, 24(1):10-2.
220
221 Karlin S., and Mrazek J. (2000) Predicted highly expressed genes of diverse
222 prokaryotic genomes J.Bacteriol, 182(18):5238-5250.
223
224 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
225 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
226 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
227
228 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
229 large-scale analysis of high-throughput omics data, J. Pest Sci.,
230 31, 7.
231
232 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
233 Analysis Environment with REST and SOAP Web Service Interfaces,
234 Nucleic Acids Res., 38, W700-W705.
235
236 </pre>
237
238 <h2>Warnings</h2>
239
240 <p>
241 None.
242 </p>
243
244 <h2>Diagnostic Error Messages</h2>
245
246 <p>
247 None.
248 </p>
249
250 <h2>Exit status</h2>
251
252 <p>
253 It always exits with a status of 0.
254 </p>
255
256 <h2>Known bugs</h2>
257
258 <p>
259 None.
260 </p>
261
262 <h2>See also</h2>
263
264 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
265 <th>Description</th></tr>
266
267 <tr>
268 <td><a href="gcai.html">gcai</a></td>
269 <td>Calculate codon adaptation index for each gene</td>
270 </tr><tr>
271 <td><a href="gp2.html">gp2</a></td>
272 <td>Calculate the P2 index of each gene</td>
273 </tr>
274
275 </table>
276
277 <h2>Author(s)</h2>
278
279 <pre>
280 Hidetoshi Itaya (celery@g-language.org)
281 Institute for Advanced Biosciences, Keio University
282 252-0882 Japan
283
284 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
285 Institute for Advanced Biosciences, Keio University
286 252-0882 Japan</pre>
287
288 <h2>History</h2>
289
290 2012 - Written by Hidetoshi Itaya
291
292 <h2>Target users</h2>
293
294 This program is intended to be used by everyone and everything, from
295 naive users to embedded scrips.
296
297 <h2>Comments</h2>
298
299 None.
300
301 </BODY>
302 </HTML>