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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gbasezvalue </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 gbasezvalue
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 Extracts conserved oligomers per position using Z-score
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 This function calculates and extracts conserved oligomers per position using<br />
45 Z-score, in regions around the start/stop codons. The oligomers are returned<br />
46 in ranking order up to "-limit" number.<br />
47 <br />
48 G-language SOAP service is provided by the<br />
49 Institute for Advanced Biosciences, Keio University.<br />
50 The original web service is located at the following URL:<br />
51 <br />
52 http://www.g-language.org/wiki/soap<br />
53 <br />
54 WSDL(RPC/Encoded) file is located at:<br />
55 <br />
56 http://soap.g-language.org/g-language.wsdl<br />
57 <br />
58 Documentation on G-language Genome Analysis Environment methods are<br />
59 provided at the Document Center<br />
60 <br />
61 http://ws.g-language.org/gdoc/<br />
62 <br />
63
64 </p>
65
66 <H2>Usage</H2>
67
68 Here is a sample session with gbasezvalue
69
70 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
71
72 % gbasezvalue refseqn:NC_000913
73 Extracts conserved oligomers per position using Z-score
74 Program compseq output file (optional) [nc_000913.gbasezvalue]:
75
76 </pre></td></tr></table>
77
78 Go to the <a href="#input">input files</a> for this example<br>
79 Go to the <a href="#output">output files</a> for this example<br><br>
80
81
82
83 <h2>Command line arguments</h2>
84
85 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
86 <tr bgcolor="#FFFFCC">
87 <th align="left">Qualifier</th>
88 <th align="left">Type</th>
89 <th align="left">Description</th>
90 <th align="left">Allowed values</th>
91 <th align="left">Default</th>
92 </tr>
93
94 <tr bgcolor="#FFFFCC">
95 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
96 </tr>
97
98 <tr bgcolor="#FFFFCC">
99 <td>[-sequence]<br>(Parameter 1)</td>
100 <td>seqall</td>
101 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
102 <td>Readable sequence(s)</td>
103 <td><b>Required</b></td>
104 </tr>
105
106 <tr bgcolor="#FFFFCC">
107 <td>[-outfile]<br>(Parameter 2)</td>
108 <td>outfile</td>
109 <td>Program compseq output file (optional)</td>
110 <td>Output file</td>
111 <td><i>&lt;*&gt;</i>.gbasezvalue</td>
112 </tr>
113
114 <tr bgcolor="#FFFFCC">
115 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
116 </tr>
117
118 <tr>
119 <td colspan=5>(none)</td>
120 </tr>
121
122 <tr bgcolor="#FFFFCC">
123 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
124 </tr>
125
126 <tr bgcolor="#FFFFCC">
127 <td>-limit</td>
128 <td>integer</td>
129 <td>Rank threshold for showing the conserved oligomer</td>
130 <td>Any integer value</td>
131 <td>5</td>
132 </tr>
133
134 <tr bgcolor="#FFFFCC">
135 <td>-position</td>
136 <td>selection</td>
137 <td>Either 'start' (around start codon) or 'end' (around stop codon) to create the PWM</td>
138 <td>Choose from selection list of values</td>
139 <td>start</td>
140 </tr>
141
142 <tr bgcolor="#FFFFCC">
143 <td>-patlen</td>
144 <td>integer</td>
145 <td>Length of oligomer to count</td>
146 <td>Any integer value</td>
147 <td>3</td>
148 </tr>
149
150 <tr bgcolor="#FFFFCC">
151 <td>-upstream</td>
152 <td>integer</td>
153 <td>Length upstream of specified position to create PWM</td>
154 <td>Any integer value</td>
155 <td>30</td>
156 </tr>
157
158 <tr bgcolor="#FFFFCC">
159 <td>-downstream</td>
160 <td>integer</td>
161 <td>Length downstream of specified position to create PWM</td>
162 <td>Any integer value</td>
163 <td>30</td>
164 </tr>
165
166 <tr bgcolor="#FFFFCC">
167 <td>-[no]accid</td>
168 <td>boolean</td>
169 <td>Include to use sequence accession ID as query</td>
170 <td>Boolean value Yes/No</td>
171 <td>Yes</td>
172 </tr>
173
174 </table>
175
176
177 <h2 id="input">Input file format</h2>
178
179 <p>
180 The database definitions for following commands are available at<br />
181 http://soap.g-language.org/kbws/embossrc<br />
182 <br />
183 gbasezvalue reads one or more nucleotide sequences.<br />
184 <br />
185
186 </p>
187
188 <h2 id="output">Output file format</h3>
189
190 <p>
191 The output from gbasezvalue is to a plain text file.<br />
192 <br />
193 File: nc_000913.gbasezvalue<br />
194 <br />
195 <table width="90%"><tr><td bgcolor="#CCFFCC">
196 Sequence: NC_000913<br />
197 position:-30,1,taa,-0.76525<br />
198 2,aga,-0.79101<br />
199 3,tta,-1.14174<br />
200 4,cta,-1.18831<br />
201 5,aat,-1.86652<br />
202 position:-29,1,cta,-0.18368<br />
203 2,aat,-0.71851<br />
204 3,gac,-1.26182<br />
205 4,taa,-1.39455<br />
206 <br />
207 <font color=red>[Part of this file has been deleted for brevity]</font><br />
208 <br />
209 position:29,1,gct,1.66288<br />
210 2,act,1.26637<br />
211 3,tat,0.66721<br />
212 4,cct,-0.43158<br />
213 5,tgt,-0.59254<br />
214 position:30,1,ctg,3.12072<br />
215 2,att,0.04193<br />
216 3,ctc,-0.12416<br />
217 4,cta,-0.38461<br />
218 5,tta,-0.76413<br />
219 </td></tr></table>
220
221 </p>
222
223 <h2>Data files</h2>
224
225 <p>
226 None.
227 </p>
228
229 <h2>Notes</h2>
230
231 <p>
232 None.
233 </p>
234
235 <h2>References</h2>
236
237 <pre>
238 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
239 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
240 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
241
242 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
243 large-scale analysis of high-throughput omics data, J. Pest Sci.,
244 31, 7.
245
246 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
247 Analysis Environment with REST and SOAP Web Service Interfaces,
248 Nucleic Acids Res., 38, W700-W705.
249
250 </pre>
251
252 <h2>Warnings</h2>
253
254 <p>
255 None.
256 </p>
257
258 <h2>Diagnostic Error Messages</h2>
259
260 <p>
261 None.
262 </p>
263
264 <h2>Exit status</h2>
265
266 <p>
267 It always exits with a status of 0.
268 </p>
269
270 <h2>Known bugs</h2>
271
272 <p>
273 None.
274 </p>
275
276 <h2>See also</h2>
277
278 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
279 <th>Description</th></tr>
280
281 <tr>
282 <td><a href="gbase_counter.html">gbase_counter</a></td>
283 <td>Creates a position weight matrix of oligomers around start codon</td>
284 </tr><tr>
285 <td><a href="gview_cds.html">gview_cds</a></td>
286 <td>Displays a graph of nucleotide contents around start and stop codons</td>
287 </tr>
288
289 </table>
290
291 <h2>Author(s)</h2>
292
293 <pre>
294 Hidetoshi Itaya (celery@g-language.org)
295 Institute for Advanced Biosciences, Keio University
296 252-0882 Japan
297
298 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
299 Institute for Advanced Biosciences, Keio University
300 252-0882 Japan</pre>
301
302 <h2>History</h2>
303
304 2012 - Written by Hidetoshi Itaya
305
306 <h2>Target users</h2>
307
308 This program is intended to be used by everyone and everything, from
309 naive users to embedded scrips.
310
311 <h2>Comments</h2>
312
313 None.
314
315 </BODY>
316 </HTML>