Mercurial > repos > ktnyt > gembassy

comparison GEMBASSY-1.0.3/doc/html/gqueryarm.html @ 2:8947fca5f715 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
Uploaded
author ktnyt
date Fri, 26 Jun 2015 05:21:44 -0400
parents 84a17b3fad1f
children
comparison
equal deleted inserted replaced
1:84a17b3fad1f 2:8947fca5f715
1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gqueryarm </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 gqueryarm
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 replication arm name (left or right) 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 gqueryarm returns whether the given position is in the left or right arm of<br />
45 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 gqueryarm
68
69 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
70
71 % gqueryarm refseqn:NC_000913 1234
72 Get the replication arm name (left or right) from the given position
73 Output file [nc_000913.gqueryarm]:
74
75 </pre></td></tr></table>
76
77
78
79 <h2>Command line arguments</h2>
80
81 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
82 <tr bgcolor="#FFFFCC">
83 <th align="left">Qualifier</th>
84 <th align="left">Type</th>
85 <th align="left">Description</th>
86 <th align="left">Allowed values</th>
87 <th align="left">Default</th>
88 </tr>
89
90 <tr bgcolor="#FFFFCC">
91 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
92 </tr>
93
94 <tr bgcolor="#FFFFCC">
95 <td>[-sequence]<br>(Parameter 1)</td>
96 <td>seqall</td>
97 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
98 <td>Readable sequence(s)</td>
99 <td><b>Required</b></td>
100 </tr>
101
102 <tr bgcolor="#FFFFCC">
103 <td>[-position]<br>(Parameter 2)</td>
104 <td>integer</td>
105 <td>Position to query</td>
106 <td>Any integer value</td>
107 <td>0</td>
108 </tr>
109
110 <tr bgcolor="#FFFFCC">
111 <td>[-outfile]<br>(Parameter 3)</td>
112 <td>outfile</td>
113 <td>Output file name</td>
114 <td>Output file</td>
115 <td><i>&lt;*&gt;</i>.gqueryarm</td>
116 </tr>
117
118 <tr bgcolor="#FFFFCC">
119 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
120 </tr>
121
122 <tr>
123 <td colspan=5>(none)</td>
124 </tr>
125
126 <tr bgcolor="#FFFFCC">
127 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
128 </tr>
129
130 <tr bgcolor="#FFFFCC">
131 <td>-[no]accid</td>
132 <td>boolean</td>
133 <td>Include to use sequence accession ID as query</td>
134 <td>Boolean value Yes/No</td>
135 <td>Yes</td>
136 </tr>
137
138 </table>
139
140
141 <h2 id="input">Input file format</h2>
142
143 <p>
144 The database definitions for following commands are available at<br />
145 http://soap.g-language.org/kbws/embossrc<br />
146 <br />
147 gqueryarm reads one or more nucleotide sequences.<br />
148 <br />
149
150 </p>
151
152 <h2 id="output">Output file format</h2>
153
154 <p>
155 The output from gqueryarm is to a plain text file.<br />
156 <br />
157 File: nc_000913.gqueryarm<br />
158 <br />
159 <table width="90%"><tr><td bgcolor="#CCFFCC">
160 Sequence: NC_000913 Arm: right<br />
161 </td></tr></table>
162
163 </p>
164
165 <h2>Data files</h2>
166
167 <p>
168 None.
169 </p>
170
171 <h2>Notes</h2>
172
173 <p>
174 None.
175 </p>
176
177 <h2>References</h2>
178
179 <pre>
180 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
181 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
182 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
183
184 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
185 large-scale analysis of high-throughput omics data, J. Pest Sci.,
186 31, 7.
187
188 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
189 Analysis Environment with REST and SOAP Web Service Interfaces,
190 Nucleic Acids Res., 38, W700-W705.
191
192 </pre>
193
194 <h2>Warnings</h2>
195
196 <p>
197 None.
198 </p>
199
200 <h2>Diagnostic Error Messages</h2>
201
202 <p>
203 None.
204 </p>
205
206 <h2>Exit status</h2>
207
208 <p>
209 It always exits with a status of 0.
210 </p>
211
212 <h2>Known bugs</h2>
213
214 <p>
215 None.
216 </p>
217
218 <h2>See also</h2>
219
220 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
221 <th>Description</th></tr>
222
223 <tr>
224 <td><a href="gquerystrand.html">gquerystrand</a></td>
225 <td>Get the strand name (leading or lagging) from the given</td>
226 </tr>
227
228 </table>
229
230 <h2>Author(s)</h2>
231
232 <pre>
233 Hidetoshi Itaya (celery@g-language.org)
234 Institute for Advanced Biosciences, Keio University
235 252-0882 Japan
236
237 Kazuharua Arakawa (gaou@sfc.keio.ac.jp)
238 Institute for Advanced Biosciences, Keio University
239 252-0882 Japan</pre>
240
241 <h2>History</h2>
242
243 2012 - Written by Hidetoshi Itaya
244
245 <h2>Target users</h2>
246
247 This program is intended to be used by everyone and everything, from
248 naive users to embedded scrips.
249
250 <h2>Comments</h2>
251
252 None.
253
254 </BODY>
255 </HTML>