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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: gentrez </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 gentrez
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 Search NCBI Entrez
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 gentrez searches NCBI Entrez with keyword through EUtilities. <br />
45 This is intended for quick lookup through the command line<br />
46 so only top ten hits are reported.<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 gentrez
69
70 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
71
72 % gentrez genome 'Escherichia coli'
73 Search NCBI Entrez
74 ASCII text output file [genome.Escherichia coli.gentrez]:
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>[-database]<br>(Parameter 1)</td>
98 <td>string</td>
99 <td>NCBI database to search</td>
100 <td>Any string</td>
101 <td>pubmed</td>
102 </tr>
103
104 <tr bgcolor="#FFFFCC">
105 <td>[-query]<br>(Parameter 2)</td>
106 <td>string</td>
107 <td>Query to search</td>
108 <td>Any string</td>
109 <td>&nbsp;</td>
110 </tr>
111
112 <tr bgcolor="#FFFFCC">
113 <td>[-outfile]<br>(Parameter 3)</td>
114 <td>outfile</td>
115 <td>ASCII text output file</td>
116 <td>Output file</td>
117 <td>$(database).$(query).gentrez</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>
133 <td colspan=5>(none)</td>
134 </tr>
135
136 </table>
137
138
139 <h2 id="input">Input file format</h2>
140
141 <p>
142 The database definitions for following commands are available at<br />
143 http://soap.g-language.org/kbws/embossrc<br />
144 <br />
145 gentrez reads no file input.<br />
146 <br />
147
148 </p>
149
150 <h2 id="output">Output file format</h2>
151
152 <p>
153 The output from gentrez is to a plain text file.<br />
154 <br />
155 File: genome.Escherichia coli.gentrez<br />
156 <br />
157 <table width="90%"><tr><td bgcolor="#CCFFCC">
158 53 entries found in NUCLEOTIDE: (Showing up to 10 hits)<br />
159 <br />
160 1. Accession Number: NZ_AKBV01000001<br />
161 Escherichia coli str. K-12 substr. MG1655 strain K-12 cont1.1 chromosome, whole genome shotgun sequence, complete genome<br />
162 <br />
163 2. Accession Number: NC_018658<br />
164 Escherichia coli O104:H4 str. 2011C-3493 chromosome, complete genome<br />
165 <br />
166 3. Accession Number: NC_012971<br />
167 Escherichia coli BL21(DE3) chromosome, complete genome<br />
168 <br />
169 4. Accession Number: NC_017635<br />
170 Escherichia coli W chromosome, complete genome<br />
171 <br />
172 5. Accession Number: NC_018650<br />
173 Escherichia coli O104:H4 str. 2009EL-2050 chromosome, complete genome<br />
174 <br />
175 6. Accession Number: NC_018661<br />
176 Escherichia coli O104:H4 str. 2009EL-2071 chromosome, complete genome<br />
177 <br />
178 7. Accession Number: NC_017906<br />
179 Escherichia coli Xuzhou21 chromosome, complete genome<br />
180 <br />
181 8. Accession Number: NC_017634<br />
182 Escherichia coli O83:H1 str. NRG 857C chromosome, complete genome<br />
183 <br />
184 9. Accession Number: NC_017656<br />
185 Escherichia coli O55:H7 str. RM12579 chromosome, complete genome<br />
186 <br />
187 10. Accession Number: NC_017664<br />
188 Escherichia coli W chromosome, complete genome<br />
189 </td></tr></table>
190
191 </p>
192
193 <h2>Data files</h2>
194
195 <p>
196 None.
197 </p>
198
199 <h2>Notes</h2>
200
201 <p>
202 None.
203 </p>
204
205 <h2>References</h2>
206
207 <pre>
208 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
209 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
210 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
211
212 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
213 large-scale analysis of high-throughput omics data, J. Pest Sci.,
214 31, 7.
215
216 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
217 Analysis Environment with REST and SOAP Web Service Interfaces,
218 Nucleic Acids Res., 38, W700-W705.
219
220 </pre>
221
222 <h2>Warnings</h2>
223
224 <p>
225 None.
226 </p>
227
228 <h2>Diagnostic Error Messages</h2>
229
230 <p>
231 None.
232 </p>
233
234 <h2>Exit status</h2>
235
236 <p>
237 It always exits with a status of 0.
238 </p>
239
240 <h2>Known bugs</h2>
241
242 <p>
243 None.
244 </p>
245
246 <h2>See also</h2>
247
248 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
249 <th>Description</th></tr>
250
251
252
253 </table>
254
255 <h2>Author(s)</h2>
256
257 <pre>
258 Hidetoshi Itaya (celery@g-language.org)
259 Institute for Advanced Biosciences, Keio University
260 252-0882 Japan
261
262 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
263 Institute for Advanced Biosciences, Keio University
264 252-0882 Japan</pre>
265
266 <h2>History</h2>
267
268 2012 - Written by Hidetoshi Itaya
269
270 <h2>Target users</h2>
271
272 This program is intended to be used by everyone and everything, from
273 naive users to embedded scrips.
274
275 <h2>Comments</h2>
276
277 None.
278
279 </BODY>
280 </HTML>