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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: gdistincc </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 gdistincc
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 distance between two loci in circular chromosomes
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 gdistincc calculates the distance between two loci in circular<br />
45 chromosomes. It is mostly useful to calculate the distance from the<br />
46 replication origin.<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 gdistincc
69
70 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
71
72 % gdistincc refseqn:NC_000913 1234
73 Calculates the distance between two loci in circular chromosomes
74 Output file [nc_000913.gdistincc]:
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 <h2>Command line arguments</h2>
82
83 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
84 <tr bgcolor="#FFFFCC">
85 <th align="left">Qualifier</th>
86 <th align="left">Type</th>
87 <th align="left">Description</th>
88 <th align="left">Allowed values</th>
89 <th align="left">Default</th>
90 </tr>
91
92 <tr bgcolor="#FFFFCC">
93 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
94 </tr>
95
96 <tr bgcolor="#FFFFCC">
97 <td>[-sequence]<br>(Parameter 1)</td>
98 <td>seqall</td>
99 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
100 <td>Readable sequence(s)</td>
101 <td><b>Required</b></td>
102 </tr>
103
104 <tr bgcolor="#FFFFCC">
105 <td>[-first]<br>(Parameter 2)</td>
106 <td>integer</td>
107 <td>Position to find the distance</td>
108 <td>Any integer value</td>
109 <td>0</td>
110 </tr>
111
112 <tr bgcolor="#FFFFCC">
113 <td>[-outfile]<br>(Parameter 3)</td>
114 <td>outfile</td>
115 <td>Output file name</td>
116 <td>Output file</td>
117 <td><i>&lt;*&gt;</i>.gdistincc</td>
118 </tr>
119
120 <tr bgcolor="#FFFFCC">
121 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
122 </tr>
123
124 <tr>
125 <td colspan=5>(none)</td>
126 </tr>
127
128 <tr bgcolor="#FFFFCC">
129 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
130 </tr>
131
132 <tr bgcolor="#FFFFCC">
133 <td>-second</td>
134 <td>integer</td>
135 <td>If the second position is negative, position of replication origin is used</td>
136 <td>Any integer value</td>
137 <td>-1</td>
138 </tr>
139
140 <tr bgcolor="#FFFFCC">
141 <td>-[no]accid</td>
142 <td>boolean</td>
143 <td>Include to use sequence accession ID as query</td>
144 <td>Boolean value Yes/No</td>
145 <td>Yes</td>
146 </tr>
147
148 </table>
149
150
151 <h2 id="input">Input file format</h2>
152
153 <p>
154 The database definitions for following commands are available at<br />
155 http://soap.g-language.org/kbws/embossrc<br />
156 <br />
157 gdistincc reads one or more nucleotide sequences.<br />
158 <br />
159
160 </p>
161
162 <h2 id="output">Output file format</h2>
163
164 <p>
165 The output from gdistincc is to a plain text file.<br />
166 <br />
167 File: nc_000913.gdistincc<br />
168 <br />
169 <table width="90%"><tr><td bgcolor="#CCFFCC">
170 Sequence: NC_000913 Position1: 1234 Distance 1169193600<br />
171 </td></tr></table>
172
173 </p>
174
175 <h2>Data files</h2>
176
177 <p>
178 None.
179 </p>
180
181 <h2>Notes</h2>
182
183 <p>
184 None.
185 </p>
186
187 <h2>References</h2>
188
189 <pre>
190 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
191 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
192 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
193
194 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
195 large-scale analysis of high-throughput omics data, J. Pest Sci.,
196 31, 7.
197
198 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
199 Analysis Environment with REST and SOAP Web Service Interfaces,
200 Nucleic Acids Res., 38, W700-W705.
201
202 </pre>
203
204 <h2>Warnings</h2>
205
206 <p>
207 None.
208 </p>
209
210 <h2>Diagnostic Error Messages</h2>
211
212 <p>
213 None.
214 </p>
215
216 <h2>Exit status</h2>
217
218 <p>
219 It always exits with a status of 0.
220 </p>
221
222 <h2>Known bugs</h2>
223
224 <p>
225 None.
226 </p>
227
228 <h2>See also</h2>
229
230 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
231 <th>Description</th></tr>
232
233 <tr>
234 <td><a href="gconsensusz.html">gconsensusz</a></td>
235 <td>Calculate consensus in given array of sequences</td>
236 </tr><tr>
237 <td><a href="gpalindrome.html">gpalindrome</a></td>
238 <td>Searches palindrome sequences</td>
239 </tr><tr>
240 <td><a href="gseqinfo.html">gseqinfo</a></td>
241 <td>Prints out basic nucleotide sequence statistics</td>
242 </tr>
243
244 </table>
245
246 <h2>Author(s)</h2>
247
248 <pre>
249 Hidetoshi Itaya (celery@g-language.org)
250 Institute for Advanced Biosciences, Keio University
251 252-0882 Japan
252
253 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
254 Institute for Advanced Biosciences, Keio University
255 252-0882 Japan</pre>
256
257 <h2>History</h2>
258
259 2012 - Written by Hidetoshi Itaya
260
261 <h2>Target users</h2>
262
263 This program is intended to be used by everyone and everything, from
264 naive users to embedded scrips.
265
266 <h2>Comments</h2>
267
268 None.
269
270 </BODY>
271 </HTML>