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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: gscs </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 gscs
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 Calculates the scaled chi-square
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 gscs calculates the Scaled Chi Square (SCS) of each gene. Values of SCS<br />
45 are calculated using completely synonymous codon usage as the expectation<br />
46 and then scaled by dividing the value by the number of codons in the gene<br />
47 excluding Trp and Met.<br />
48 <br />
49 G-language SOAP service is provided by the<br />
50 Institute for Advanced Biosciences, Keio University.<br />
51 The original web service is located at the following URL:<br />
52 <br />
53 http://www.g-language.org/wiki/soap<br />
54 <br />
55 WSDL(RPC/Encoded) file is located at:<br />
56 <br />
57 http://soap.g-language.org/g-language.wsdl<br />
58 <br />
59 Documentation on G-language Genome Analysis Environment methods are<br />
60 provided at the Document Center<br />
61 <br />
62 http://ws.g-language.org/gdoc/<br />
63 <br />
64
65 </p>
66
67 <H2>Usage</H2>
68
69 Here is a sample session with gscs
70
71 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
72
73 % gscs refseqn:NC_000913
74 Calculates the scaled chi-square
75 Codon usage output file [nc_000913.gscs]:
76
77 </pre></td></tr></table>
78
79 Go to the <a href="#input">input files</a> for this example<br>
80 Go to the <a href="#output">output files</a> for this example<br><br>
81
82 <h2>Command line arguments</h2>
83
84 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
85 <tr bgcolor="#FFFFCC">
86 <th align="left">Qualifier</th>
87 <th align="left">Type</th>
88 <th align="left">Description</th>
89 <th align="left">Allowed values</th>
90 <th align="left">Default</th>
91 </tr>
92
93 <tr bgcolor="#FFFFCC">
94 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
95 </tr>
96
97 <tr bgcolor="#FFFFCC">
98 <td>[-sequence]<br>(Parameter 1)</td>
99 <td>seqall</td>
100 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
101 <td>Readable sequence(s)</td>
102 <td><b>Required</b></td>
103 </tr>
104
105 <tr bgcolor="#FFFFCC">
106 <td>[-outfile]<br>(Parameter 2)</td>
107 <td>outfile</td>
108 <td>Codon usage output file</td>
109 <td>Output file</td>
110 <td><i>&lt;*&gt;</i>.gscs</td>
111 </tr>
112
113 <tr bgcolor="#FFFFCC">
114 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
115 </tr>
116
117 <tr>
118 <td colspan=5>(none)</td>
119 </tr>
120
121 <tr bgcolor="#FFFFCC">
122 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
123 </tr>
124
125 <tr bgcolor="#FFFFCC">
126 <td>-translate</td>
127 <td>boolean</td>
128 <td>Include when translates using standard codon table</td>
129 <td>Boolean value Yes/No</td>
130 <td>No</td>
131 </tr>
132
133 <tr bgcolor="#FFFFCC">
134 <td>-delkey</td>
135 <td>string</td>
136 <td>Regular expression to delete key (i.e. amino acids and nucleotides)</td>
137 <td>Any string</td>
138 <td>[^ACDEFGHIKLMNPQRSTVWYacgtU]</td>
139 </tr>
140
141 <tr bgcolor="#FFFFCC">
142 <td>-[no]accid</td>
143 <td>boolean</td>
144 <td>Include to use sequence accession ID as query</td>
145 <td>Boolean value Yes/No</td>
146 <td>Yes</td>
147 </tr>
148
149 </table>
150
151
152 <h2 id="input">Input file format</h2>
153
154 <p>
155 The database definitions for following commands are available at<br />
156 http://soap.g-language.org/kbws/embossrc<br />
157 <br />
158 gscs reads one or more nucleotide sequences.<br />
159 <br />
160
161 </p>
162
163 <h2 id="output">Output file format</h2>
164
165 <p>
166 The output from gscs is to a plain text file.<br />
167 <br />
168 File: nc_000913.gscs<br />
169 <br />
170 <table width="90%"><tr><td bgcolor="#CCFFCC">
171 Sequence: NC_000913<br />
172 scs,gene<br />
173 1.4458,thrL<br />
174 0.3122,thrA<br />
175 0.2551,thrB<br />
176 0.4104,thrC<br />
177 0.3084,yaaX<br />
178 0.3230,yaaA<br />
179 0.2957,yaaJ<br />
180 0.7101,talB<br />
181 <br />
182 [Part of this file has been deleted for brevity]<br />
183 <br />
184 0.3054,yjjX<br />
185 0.4076,ytjC<br />
186 0.4231,rob<br />
187 0.3903,creA<br />
188 0.3472,creB<br />
189 0.2695,creC<br />
190 0.3500,creD<br />
191 0.5077,arcA<br />
192 0.4576,yjjY<br />
193 0.2926,yjtD<br />
194 </td></tr></table>
195
196 </p>
197
198 <h2>Data files</h2>
199
200 <p>
201 None.
202 </p>
203
204 <h2>Notes</h2>
205
206 <p>
207 None.
208 </p>
209
210 <h2>References</h2>
211
212 <pre>
213 Comeron JM., Aguade M. (1998) An evaluation of measures of synonymous
214 codon usage bias, J Mol Evol, 47(3):268-74.
215
216 Shields DC, Sharp PM. (1987) Synonymous codon usage in Bacillus subtilis
217 reflects both translational selection and mutational biases,
218 15(19):8023-40.
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="genc.html">genc</a></td>
265 <td>Calculate the effective number of codons (Nc)</td>
266 </tr><tr>
267 <td><a href="gew.html">gew</a></td>
268 <td>Calculate a measure of synonymous codon usage evenness (Ew)</td>
269 </tr><tr>
270 <td><a href="gfop.html">gfop</a></td>
271 <td>Calculate the frequency of optimal codons (Fop)</td>
272 </tr><tr>
273 <td><a href="gwvalue.html">gwvalue</a></td>
274 <td>Calculate the 'relative adaptiveness of each codon' (W)</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>