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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: gseqinfo </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 gseqinfo
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 Prints out basic nucleotide sequence statistics
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 gseqinfo prints out basic nucleotide sequence statistics of the given<br />
45 nucleotide sequence. It returns the number of A, T, G, and C bases.<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 gseqinfo
68
69 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
70
71 % gseqinfo refseqn:NC_000913
72 Prints out basic nucleotide sequence statistics
73 Program compseq output file [nc_000913.gseqinfo]:
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>[-outfile]<br>(Parameter 2)</td>
105 <td>outfile</td>
106 <td>Program compseq output file</td>
107 <td>Output file</td>
108 <td><i>&lt;*&gt;</i>.gseqinfo</td>
109 </tr>
110
111 <tr bgcolor="#FFFFCC">
112 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
113 </tr>
114
115 <tr>
116 <td colspan=5>(none)</td>
117 </tr>
118
119 <tr bgcolor="#FFFFCC">
120 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
121 </tr>
122
123 <tr>
124 <td colspan=5>(none)</td>
125 </tr>
126
127 </table>
128
129
130 <h2 id="input">Input file format</h2>
131
132 <p>
133 The database definitions for following commands are available at<br />
134 http://soap.g-language.org/kbws/embossrc<br />
135 <br />
136 gseqinfo reads one or more nucleotide sequences.<br />
137 <br />
138
139 </p>
140
141 <h2 id="output">Output file format</h2>
142
143 <p>
144 The output from gseqinfo is to a plain text file.<br />
145 <br />
146 File: nc_000913.gseqinfo<br />
147 <br />
148 <table width="90%"><tr><td bgcolor="#CCFFCC">
149 Sequence: NC_000913 A: 1142228 T: 1140970 G: 1176923 C: 1179555<br />
150 </td></tr></table>
151
152 </p>
153
154 <h2>Data files</h2>
155
156 <p>
157 None.
158 </p>
159
160 <h2>Notes</h2>
161
162 <p>
163 None.
164 </p>
165
166 <h2>References</h2>
167
168 <pre>
169 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
170 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
171 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
172
173 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
174 large-scale analysis of high-throughput omics data, J. Pest Sci.,
175 31, 7.
176
177 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
178 Analysis Environment with REST and SOAP Web Service Interfaces,
179 Nucleic Acids Res., 38, W700-W705.
180
181 </pre>
182
183 <h2>Warnings</h2>
184
185 <p>
186 None.
187 </p>
188
189 <h2>Diagnostic Error Messages</h2>
190
191 <p>
192 None.
193 </p>
194
195 <h2>Exit status</h2>
196
197 <p>
198 It always exits with a status of 0.
199 </p>
200
201 <h2>Known bugs</h2>
202
203 <p>
204 None.
205 </p>
206
207 <h2>See also</h2>
208
209 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
210 <th>Description</th></tr>
211
212 <tr>
213 <td><a href="gconsensusz.html">gconsensusz</a></td>
214 <td>Calculate consensus in given array of sequences</td>
215 </tr><tr>
216 <td><a href="gdistincc.html">gdistincc</a></td>
217 <td>Calculates the distance between two loci in circular chromosomes</td>
218 </tr><tr>
219 <td><a href="gpalindrome.html">gpalindrome</a></td>
220 <td>Searches palindrome sequences</td>
221 </tr>
222
223 </table>
224
225 <h2>Author(s)</h2>
226
227 <pre>
228 Hidetoshi Itaya (celery@g-language.org)
229 Institute for Advanced Biosciences, Keio University
230 252-0882 Japan
231
232 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
233 Institute for Advanced Biosciences, Keio University
234 252-0882 Japan</pre>
235
236 <h2>History</h2>
237
238 2012 - Written by Hidetoshi Itaya
239
240 <h2>Target users</h2>
241
242 This program is intended to be used by everyone and everything, from
243 naive users to embedded scrips.
244
245 <h2>Comments</h2>
246
247 None.
248
249 </BODY>
250 </HTML>