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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gcodoncompiler </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 gcodoncompiler
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 various kinds of amino acid and codon usage data
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 gcodoncompiler calculates various kinds of amino acid and codon usage data.<br />
45 The following values are calculable:<br />
46 A0: Absolute amino acid frequency<br />
47 A1: Relative amino acid frequency<br />
48 C0: Absolute codon frequency<br />
49 C1: Relative codon frequency in a complete sequence<br />
50 C2: Relative codon frequency in each amino acid<br />
51 C3: Relative synonymous codon usage<br />
52 C4: Relative adaptiveness<br />
53 C5: Maximum or minor codon<br />
54 For amino acids unpresent in a gene, C2-C3 does not calculate the values.<br />
55 By using R* in place, such values are hypothesized that alternative<br />
56 synonymous codons are used with equal frequency.<br />
57 <br />
58 G-language SOAP service is provided by the<br />
59 Institute for Advanced Biosciences, Keio University.<br />
60 The original web service is located at the following URL:<br />
61 <br />
62 http://www.g-language.org/wiki/soap<br />
63 <br />
64 WSDL(RPC/Encoded) file is located at:<br />
65 <br />
66 http://soap.g-language.org/g-language.wsdl<br />
67 <br />
68 Documentation on G-language Genome Analysis Environment methods are<br />
69 provided at the Document Center<br />
70 <br />
71 http://ws.g-language.org/gdoc/<br />
72 <br />
73
74 </p>
75
76 <H2>Usage</H2>
77
78 Here is a sample session with gcodoncompiler
79
80 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
81
82 % gcodoncompiler refseqn:NC_000913
83 Calculate various kinds of amino acid and codon usage data
84 Codon usage output file [nc_000913.gcodoncompiler]:
85
86 </pre></td></tr></table>
87
88 Go to the <a href="#input">input files</a> for this example<br>
89 Go to the <a href="#output">output files</a> for this example<br><br>
90
91 <h2>Command line arguments</h2>
92
93 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
94 <tr bgcolor="#FFFFCC">
95 <th align="left">Qualifier</th>
96 <th align="left">Type</th>
97 <th align="left">Description</th>
98 <th align="left">Allowed values</th>
99 <th align="left">Default</th>
100 </tr>
101
102 <tr bgcolor="#FFFFCC">
103 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
104 </tr>
105
106 <tr bgcolor="#FFFFCC">
107 <td>[-sequence]<br>(Parameter 1)</td>
108 <td>seqall</td>
109 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
110 <td>Readable sequence(s)</td>
111 <td><b>Required</b></td>
112 </tr>
113
114 <tr bgcolor="#FFFFCC">
115 <td>[-outfile]<br>(Parameter 2)</td>
116 <td>outfile</td>
117 <td>Codon usage output file</td>
118 <td>Output file</td>
119 <td><i>&lt;*&gt;</i>.gcodoncompiler</td>
120 </tr>
121
122 <tr bgcolor="#FFFFCC">
123 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
124 </tr>
125
126 <tr>
127 <td colspan=5>(none)</td>
128 </tr>
129
130 <tr bgcolor="#FFFFCC">
131 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
132 </tr>
133
134 <tr bgcolor="#FFFFCC">
135 <td>-translate</td>
136 <td>boolean</td>
137 <td>Include to translate using standard codon table</td>
138 <td>Boolean value Yes/No</td>
139 <td>No</td>
140 </tr>
141
142 <tr bgcolor="#FFFFCC">
143 <td>-startcodon</td>
144 <td>boolean</td>
145 <td>Include to include start codon</td>
146 <td>Boolean value Yes/No</td>
147 <td>No</td>
148 </tr>
149
150 <tr bgcolor="#FFFFCC">
151 <td>-stopcodon</td>
152 <td>boolean</td>
153 <td>Include to include stop codon</td>
154 <td>Boolean value Yes/No</td>
155 <td>No</td>
156 </tr>
157
158 <tr bgcolor="#FFFFCC">
159 <td>-delkey</td>
160 <td>string</td>
161 <td>Regular expression to delete key (i.e. amino acids and nucleotides)</td>
162 <td>Any string</td>
163 <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td>
164 </tr>
165
166 <tr bgcolor="#FFFFCC">
167 <td>-data</td>
168 <td>list</td>
169 <td>Kinds of codon usage data. R* hypothesizes amino acids which are not present in the gene</td>
170 <td><table><tr><td>A0</td> <td><i>(Absolute amino acid frequency ('AA'))</i></td></tr><tr><td>A1</td> <td><i>(Relative amino acid frequency ('RAAU'))</i></td></tr><tr><td>C0</td> <td><i>(Absolute codon frequency ('AF'))</i></td></tr><tr><td>C1</td> <td><i>(Relative codon frequency in a complete sequence)</i></td></tr><tr><td>C2</td> <td><i>(Relative codon frequency in each amino acid ('RF'))</i></td></tr><tr><td>C3</td> <td><i>(Relative synonymous codon usage ('RSCU'))</i></td></tr><tr><td>C4</td> <td><i>(Relative adaptiveness)</i></td></tr><tr><td>i.e., ratio to maximum of minor codon ('W') C5</td> <td><i>(Maximum (1) or minor (0) codon)</i></td></tr><tr><td>R0</td> <td><i>(Absolute codon frequency ('AF'))</i></td></tr><tr><td>R1</td> <td><i>(Relative codon frequency in a complete sequence)</i></td></tr><tr><td>R2</td> <td><i>(Relative codon frequency in each amino acid ('RF'))</i></td></tr><tr><td>R3</td> <td><i>(Relative synonymous codon usage ('RSCU'))</i></td></tr><tr><td>R4</td> <td><i>(Relative adaptiveness)</i></td></tr><tr><td>i.e., ratio to maximum of minor codon ('W') R5</td> <td><i>(Maximum (1) or minor (0) codon)</i></td></tr></table></td>
171 <td>R0</td>
172 </tr>
173
174 <tr bgcolor="#FFFFCC">
175 <td>-[no]accid</td>
176 <td>boolean</td>
177 <td>Include to use sequence accession ID as query</td>
178 <td>Boolean value Yes/No</td>
179 <td>Yes</td>
180 </tr>
181
182 </table>
183
184
185 <h2 id="input">Input file format</h2>
186
187 <p>
188 The database definitions for following commands are available at<br />
189 http://soap.g-language.org/kbws/embossrc<br />
190 <br />
191 gcodoncompiler reads one or more nucleotide sequences.<br />
192 <br />
193
194 </p>
195
196 <h2 id="output">Output file format</h2>
197
198 <p>
199 The output from gcodoncompiler is to a plain text file.<br />
200 <br />
201 File: nc_000913.gcodoncompiler<br />
202 <br />
203 <table width="90%"><tr><td bgcolor="#CCFFCC">
204 Sequence: NC_000913<br />
205 Agca,Agcc,Agcg,Agct,Ctgc,Ctgt,Dgac,Dgat,Egaa,Egag,Fttc,Fttt,Ggga,Gggc,Gggg,Gggt,Hcac,Hcat,Iata,Iatc,Iatt,Kaaa,Kaag,Lcta,Lctc,Lctg,Lctt,Ltta,Lttg,Matg,Naac,Naat,Pcca,Pccc,Pccg,Pcct,Qcaa,Qcag,Raga,Ragg,Rcga,Rcgc,Rcgg,Rcgt,Sagc,Sagt,Stca,Stcc,Stcg,Stct,Taca,Tacc,Tacg,Tact,Utga,Vgta,Vgtc,Vgtg,Vgtt,Wtgg,Ytac,Ytat,locus_tag<br />
206 26551,33911,44924,20010,8486,6707,25234,42161,52362,23474,21841,29334,10226,39395,14472,32678,12830,16952,5356,33359,40221,44272,13398,5079,14709,70441,14410,18097,17936,32971,28329,22786,11063,7142,30994,9130,20216,38169,2495,1366,4529,29308,6991,27864,21132,11323,9159,11332,11759,10992,8979,31001,18989,11581,3,14337,20240,34499,24056,20071,16088,21069,<br />
207 </td></tr></table>
208
209 </p>
210
211 <h2>Data files</h2>
212
213 <p>
214 None.
215 </p>
216
217 <h2>Notes</h2>
218
219 <p>
220 None.
221 </p>
222
223 <h2>References</h2>
224
225 <pre>
226 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
227 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
228 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
229
230 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
231 large-scale analysis of high-throughput omics data, J. Pest Sci.,
232 31, 7.
233
234 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
235 Analysis Environment with REST and SOAP Web Service Interfaces,
236 Nucleic Acids Res., 38, W700-W705.
237
238 </pre>
239
240 <h2>Warnings</h2>
241
242 <p>
243 None.
244 </p>
245
246 <h2>Diagnostic Error Messages</h2>
247
248 <p>
249 None.
250 </p>
251
252 <h2>Exit status</h2>
253
254 <p>
255 It always exits with a status of 0.
256 </p>
257
258 <h2>Known bugs</h2>
259
260 <p>
261 None.
262 </p>
263
264 <h2>See also</h2>
265
266 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
267 <th>Description</th></tr>
268
269 <tr>
270 <td><a href="gaminoinfo.html">gaminoinfo</a></td>
271 <td>Prints out basic amino acid sequence statistics</td>
272 </tr><tr>
273 <td><a href="gaaui.html">gaaui</a></td>
274 <td>Calculates various indece of amino acid usage</td>
275 </tr>
276
277 </table>
278
279 <h2>Author(s)</h2>
280
281 <pre>
282 Hidetoshi Itaya (celery@g-language.org)
283 Institute for Advanced Biosciences, Keio University
284 252-0882 Japan
285
286 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
287 Institute for Advanced Biosciences, Keio University
288 252-0882 Japan</pre>
289
290 <h2>History</h2>
291
292 2012 - Written by Hidetoshi Itaya
293
294 <h2>Target users</h2>
295
296 This program is intended to be used by everyone and everything, from
297 naive users to embedded scrips.
298
299 <h2>Comments</h2>
300
301 None.
302
303 </BODY>
304 </HTML>