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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: gconsensusz </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 gconsensusz
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 consensus in given array of sequences
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 gconsensusz calculates the consensus of given list of sequences, using<br />
45 Z-score. The Z-score will show higher values when the sequences are biased<br />
46 to a single character within the list.<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 gconsensusz
69
70 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
71
72 % gconsensusz consensus.fasta
73 Calculate consensus in given array of sequences
74 Program compseq output file (optional) [rs_000000.gconsensusz]:
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 Example 2
82
83 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
84
85 % gconsensusz consensus.fasta -plot -graph png
86 Calculate consensus in given array of sequences
87 Created gconsensusz.1.png
88
89 </pre></td></tr></table>
90
91 Go to the <a href="#input">input files</a> for this example<br>
92 Go to the <a href="#output">output files</a> for this example<br><br>
93
94 <h2>Command line arguments</h2>
95
96 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
97 <tr bgcolor="#FFFFCC">
98 <th align="left">Qualifier</th>
99 <th align="left">Type</th>
100 <th align="left">Description</th>
101 <th align="left">Allowed values</th>
102 <th align="left">Default</th>
103 </tr>
104
105 <tr bgcolor="#FFFFCC">
106 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
107 </tr>
108
109 <tr bgcolor="#FFFFCC">
110 <td>[-sequence]<br>(Parameter 1)</td>
111 <td>seqall</td>
112 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
113 <td>Readable sequence(s)</td>
114 <td><b>Required</b></td>
115 </tr>
116
117 <tr bgcolor="#FFFFCC">
118 <td>-graph</td>
119 <td>xygraph</td>
120 <td>Graph type</td>
121 <td>EMBOSS has a list of known devices, including ps, hpgl, hp7470, hp7580, meta, cps, x11, tek, tekt, none, data, xterm, png, gif, svg</td>
122 <td><i>EMBOSS_GRAPHICS</i> value, or x11</td>
123 </tr>
124
125 <tr bgcolor="#FFFFCC">
126 <td>-outfile</td>
127 <td>outfile</td>
128 <td>Program compseq output file (optional)</td>
129 <td>Output file</td>
130 <td><i>&lt;*&gt;</i>.gconsensusz</td>
131 </tr>
132
133 <tr bgcolor="#FFFFCC">
134 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
135 </tr>
136
137 <tr>
138 <td colspan=5>(none)</td>
139 </tr>
140
141 <tr bgcolor="#FFFFCC">
142 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
143 </tr>
144
145 <tr bgcolor="#FFFFCC">
146 <td>-high</td>
147 <td>integer</td>
148 <td>Z value greater than which is significant</td>
149 <td>Any integer value</td>
150 <td>1</td>
151 </tr>
152
153 <tr bgcolor="#FFFFCC">
154 <td>-low</td>
155 <td>float</td>
156 <td>Z value less than which is insignificant</td>
157 <td>Any numeric value</td>
158 <td>0.2</td>
159 </tr>
160
161 <tr bgcolor="#FFFFCC">
162 <td>-plot</td>
163 <td>toggle</td>
164 <td>Include to plot result</td>
165 <td>Toggle value Yes/No</td>
166 <td>No</td>
167 </tr>
168
169 </table>
170
171
172 <h2 id="input">Input file format</h2>
173
174 <p>
175 The database definitions for following commands are available at<br />
176 http://soap.g-language.org/kbws/embossrc<br />
177 <br />
178 gconsensusz reads one or more nucleotide sequences.<br />
179 <br />
180
181 </p>
182
183 <h2 id="output">Output file format</h2>
184
185 <p>
186 The output from gconsensusz is to a plain text file or the EMBOSS graphics device.<br />
187 <br />
188 File: rs_000000.gconsensusz<br />
189 <br />
190 <table width="90%"><tr><td bgcolor="#CCFFCC">
191 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/>
192 </td></tr></table>
193
194 </p>
195
196 <h2>Data files</h2>
197
198 <p>
199 None.
200 </p>
201
202 <h2>Notes</h2>
203
204 <p>
205 None.
206 </p>
207
208 <h2>References</h2>
209
210 <pre>
211 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
212 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
213 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
214
215 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
216 large-scale analysis of high-throughput omics data, J. Pest Sci.,
217 31, 7.
218
219 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
220 Analysis Environment with REST and SOAP Web Service Interfaces,
221 Nucleic Acids Res., 38, W700-W705.
222
223 </pre>
224
225 <h2>Warnings</h2>
226
227 <p>
228 None.
229 </p>
230
231 <h2>Diagnostic Error Messages</h2>
232
233 <p>
234 None.
235 </p>
236
237 <h2>Exit status</h2>
238
239 <p>
240 It always exits with a status of 0.
241 </p>
242
243 <h2>Known bugs</h2>
244
245 <p>
246 None.
247 </p>
248
249 <h2>See also</h2>
250
251 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
252 <th>Description</th></tr>
253
254 <tr>
255 <td><a href="gdistincc.html">gdistincc</a></td>
256 <td>Calculates the distance between two loci in circular chromosomes</td>
257 </tr><tr>
258 <td><a href="gpalindrome.html">gpalindrome</a></td>
259 <td>Searches palindrome sequences</td>
260 </tr><tr>
261 <td><a href="gseqinfo.html">gseqinfo</a></td>
262 <td>Prints out basic nucleotide sequence statistics</td>
263 </tr>
264
265 </table>
266
267 <h2>Author(s)</h2>
268
269 <pre>
270 Hidetoshi Itaya (celery@g-language.org)
271 Institute for Advanced Biosciences, Keio University
272 252-0882 Japan
273
274 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
275 Institute for Advanced Biosciences, Keio University
276 252-0882 Japan</pre>
277
278 <h2>History</h2>
279
280 2012 - Written by Hidetoshi Itaya
281
282 <h2>Target users</h2>
283
284 This program is intended to be used by everyone and everything, from
285 naive users to embedded scrips.
286
287 <h2>Comments</h2>
288
289 None.
290
291 </BODY>
292 </HTML>