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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: gquerystrand </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 gquerystrand
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 Get the strand name (leading or lagging) from the given position
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 gquerystrand returns whether the given position is in the leading or lagging<br />
45 strand of a circular chromosome.<br />
46 <br />
47 G-language SOAP service is provided by the<br />
48 Institute for Advanced Biosciences, Keio University.<br />
49 The original web service is located at the following URL:<br />
50 <br />
51 http://www.g-language.org/wiki/soap<br />
52 <br />
53 WSDL(RPC/Encoded) file is located at:<br />
54 <br />
55 http://soap.g-language.org/g-language.wsdl<br />
56 <br />
57 Documentation on G-language Genome Analysis Environment methods are<br />
58 provided at the Document Center<br />
59 <br />
60 http://ws.g-language.org/gdoc/<br />
61 <br />
62
63 </p>
64
65 <H2>Usage</H2>
66
67 Here is a sample session with gquerystrand
68
69 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
70
71 % gquerystrand refseqn:NC_000913 1234
72 Get the strand name (leading or lagging) from the given position
73 Output file [nc_000913.gquerystrand]:
74
75 </pre></td></tr></table>
76
77 Go to the <a href="#input">input files</a> for this example<br>
78 Go to the <a href="#output">output files</a> for this example<br><br>
79
80 <h2>Command line arguments</h2>
81
82 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
83 <tr bgcolor="#FFFFCC">
84 <th align="left">Qualifier</th>
85 <th align="left">Type</th>
86 <th align="left">Description</th>
87 <th align="left">Allowed values</th>
88 <th align="left">Default</th>
89 </tr>
90
91 <tr bgcolor="#FFFFCC">
92 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
93 </tr>
94
95 <tr bgcolor="#FFFFCC">
96 <td>[-sequence]<br>(Parameter 1)</td>
97 <td>seqall</td>
98 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
99 <td>Readable sequence(s)</td>
100 <td><b>Required</b></td>
101 </tr>
102
103 <tr bgcolor="#FFFFCC">
104 <td>[-position]<br>(Parameter 2)</td>
105 <td>integer</td>
106 <td>Position to query</td>
107 <td>Any integer value</td>
108 <td>0</td>
109 </tr>
110
111 <tr bgcolor="#FFFFCC">
112 <td>[-outfile]<br>(Parameter 3)</td>
113 <td>outfile</td>
114 <td>Output file name</td>
115 <td>Output file</td>
116 <td><i>&lt;*&gt;</i>.gquerystrand</td>
117 </tr>
118
119 <tr bgcolor="#FFFFCC">
120 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
121 </tr>
122
123 <tr>
124 <td colspan=5>(none)</td>
125 </tr>
126
127 <tr bgcolor="#FFFFCC">
128 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
129 </tr>
130
131 <tr bgcolor="#FFFFCC">
132 <td>-direction</td>
133 <td>selection</td>
134 <td>Strand of the querying position either 'direct' or 'complement'</td>
135 <td>Choose from selection list of values</td>
136 <td>direct</td>
137 </tr>
138
139 <tr bgcolor="#FFFFCC">
140 <td>-[no]accid</td>
141 <td>boolean</td>
142 <td>Include to use sequence accession ID as query</td>
143 <td>Boolean value Yes/No</td>
144 <td>Yes</td>
145 </tr>
146
147 </table>
148
149
150 <h2 id="input">Input file format</h2>
151
152 <p>
153 The database definitions for following commands are available at<br />
154 http://soap.g-language.org/kbws/embossrc<br />
155 <br />
156 gquerystrand reads one or more nucleotide sequences.<br />
157 <br />
158
159 </p>
160
161 <h2 id="output">Output file format</h2>
162
163 <p>
164 The output from gquerystrand is to a plain text file.<br />
165 <br />
166 File: nc_000913.gquerystrand<br />
167 <br />
168 <table width="90%"><tr><td bgcolor="#CCFFCC">
169 Sequence: NC_000913 Strand: leading<br />
170 </td></tr></table>
171
172 </p>
173
174 <h2>Data files</h2>
175
176 <p>
177 None.
178 </p>
179
180 <h2>Notes</h2>
181
182 <p>
183 None.
184 </p>
185
186 <h2>References</h2>
187
188 <pre>
189 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
190 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
191 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
192
193 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
194 large-scale analysis of high-throughput omics data, J. Pest Sci.,
195 31, 7.
196
197 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
198 Analysis Environment with REST and SOAP Web Service Interfaces,
199 Nucleic Acids Res., 38, W700-W705.
200
201 </pre>
202
203 <h2>Warnings</h2>
204
205 <p>
206 None.
207 </p>
208
209 <h2>Diagnostic Error Messages</h2>
210
211 <p>
212 None.
213 </p>
214
215 <h2>Exit status</h2>
216
217 <p>
218 It always exits with a status of 0.
219 </p>
220
221 <h2>Known bugs</h2>
222
223 <p>
224 None.
225 </p>
226
227 <h2>See also</h2>
228
229 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
230 <th>Description</th></tr>
231
232 <tr>
233 <td><a href="gqueryarm.html">gqueryarm</a></td>
234 <td>Get the replication arm name (left or right) from the given</td>
235 </tr>
236
237 </table>
238
239 <h2>Author(s)</h2>
240
241 <pre>
242 Hidetoshi Itaya (celery@g-language.org)
243 Institute for Advanced Biosciences, Keio University
244 252-0882 Japan
245
246 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
247 Institute for Advanced Biosciences, Keio University
248 252-0882 Japan</pre>
249
250 <h2>History</h2>
251
252 2012 - Written by Hidetoshi Itaya
253
254 <h2>Target users</h2>
255
256 This program is intended to be used by everyone and everything, from
257 naive users to embedded scrips.
258
259 <h2>Comments</h2>
260
261 None.
262
263 </BODY>
264 </HTML>