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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: goligomersearch </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 goligomersearch
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 Searches oligomers in given sequence
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 goligomersearch searches for the given oligomer in given sequence. Oligomer<br />
45 can be specified using degenerate nucleotide alphabet, or by regular<br />
46 expressions. Performance is optimized for fast searching.<br />
47 This method changes the returning value according to the given options.<br />
48 <br />
49 G-language SOAP service is provided by the<br />
50 Institute for Advanced Biosciences, Keio University.<br />
51 The original web service is located at the following URL:<br />
52 <br />
53 http://www.g-language.org/wiki/soap<br />
54 <br />
55 WSDL(RPC/Encoded) file is located at:<br />
56 <br />
57 http://soap.g-language.org/g-language.wsdl<br />
58 <br />
59 Documentation on G-language Genome Analysis Environment methods are<br />
60 provided at the Document Center<br />
61 <br />
62 http://ws.g-language.org/gdoc/<br />
63 <br />
64
65 </p>
66
67 <H2>Usage</H2>
68
69 Here is a sample session with goligomersearch
70
71 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
72
73 % goligomersearch refseqn:NC_000913 atgcatgc
74 Searches oligomers in given sequence
75 Program compseq output file [nc_000913.goligomersearch]:
76
77 </pre></td></tr></table>
78
79 Go to the <a href="#input">input files</a> for this example<br>
80 Go to the <a href="#output">output files</a> for this example<br><br>
81
82 <h2>Command line arguments</h2>
83
84 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
85 <tr bgcolor="#FFFFCC">
86 <th align="left">Qualifier</th>
87 <th align="left">Type</th>
88 <th align="left">Description</th>
89 <th align="left">Allowed values</th>
90 <th align="left">Default</th>
91 </tr>
92
93 <tr bgcolor="#FFFFCC">
94 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
95 </tr>
96
97 <tr bgcolor="#FFFFCC">
98 <td>[-sequence]<br>(Parameter 1)</td>
99 <td>seqall</td>
100 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
101 <td>Readable sequence(s)</td>
102 <td><b>Required</b></td>
103 </tr>
104
105 <tr bgcolor="#FFFFCC">
106 <td>[-oligomer]<br>(Parameter 2)</td>
107 <td>string</td>
108 <td>Oligomer to search</td>
109 <td>Any string</td>
110 <td>&nbsp;</td>
111 </tr>
112
113 <tr bgcolor="#FFFFCC">
114 <td>[-outfile]<br>(Parameter 3)</td>
115 <td>outfile</td>
116 <td>Program compseq output file</td>
117 <td>Output file</td>
118 <td><i>&lt;*&gt;</i>.goligomersearch</td>
119 </tr>
120
121 <tr bgcolor="#FFFFCC">
122 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
123 </tr>
124
125 <tr>
126 <td colspan=5>(none)</td>
127 </tr>
128
129 <tr bgcolor="#FFFFCC">
130 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
131 </tr>
132
133 <tr bgcolor="#FFFFCC">
134 <td>-return</td>
135 <td>selection</td>
136 <td>'position' to return list of positions where oligomers are found, 'oligo' to return list of oligomers found ordered by positions, 'both' to return a hash with positions as keys and oligomers as values, 'distribution' to return four values about the distribution of given oligomer</td>
137 <td>Choose from selection list of values</td>
138 <td>position</td>
139 </tr>
140
141 <tr bgcolor="#FFFFCC">
142 <td>-[no]accid</td>
143 <td>boolean</td>
144 <td>Include to use sequence accession ID as query</td>
145 <td>Boolean value Yes/No</td>
146 <td>Yes</td>
147 </tr>
148
149 </table>
150
151
152 <h2 id="input">Input file format</h2>
153
154 <p>
155 The database definitions for following commands are available at<br />
156 http://soap.g-language.org/kbws/embossrc<br />
157 <br />
158 goligomersearch reads one or more nucleotide sequences.<br />
159 <br />
160
161 </p>
162
163 <h2 id="output">Output file format</h2>
164
165 <p>
166 The output from goligomersearch is to a plain text file.<br />
167 <br />
168 File: nc_000913.goligomersearch<br />
169 <br />
170 <table width="90%"><tr><td bgcolor="#CCFFCC">
171 Sequence: NC_000913 Oligomer: atgcatgc Return: 147018,366819,653138,863326,1288615,1627117,2111200,2246695,2697278,2750962,2826906,2882353,2998362,3022134,3346029,3477018,3629113,3842819,3958304,3982183,4013480,4285578,4474663,4484501,4499080,4604562,4638391<br />
172 </td></tr></table>
173
174 </p>
175
176 <h2>Data files</h2>
177
178 <p>
179 None.
180 </p>
181
182 <h2>Notes</h2>
183
184 <p>
185 None.
186 </p>
187
188 <h2>References</h2>
189
190 <pre>
191 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
192 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
193 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
194
195 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
196 large-scale analysis of high-throughput omics data, J. Pest Sci.,
197 31, 7.
198
199 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
200 Analysis Environment with REST and SOAP Web Service Interfaces,
201 Nucleic Acids Res., 38, W700-W705.
202
203 </pre>
204
205 <h2>Warnings</h2>
206
207 <p>
208 None.
209 </p>
210
211 <h2>Diagnostic Error Messages</h2>
212
213 <p>
214 None.
215 </p>
216
217 <h2>Exit status</h2>
218
219 <p>
220 It always exits with a status of 0.
221 </p>
222
223 <h2>Known bugs</h2>
224
225 <p>
226 None.
227 </p>
228
229 <h2>See also</h2>
230
231 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
232 <th>Description</th></tr>
233
234 <tr>
235 <td><a href="gkmertable.html">gkmertable</a></td>
236 <td>Create an image showing all k-mer abundance within a sequence</td>
237 </tr><tr>
238 <td><a href="gnucleotideperiodicity.html">gnucleotideperiodicity</a></td>
239 <td>Checks the periodicity of certain oligonucleotides</td>
240 </tr><tr>
241 <td><a href="goligomercounter.html">goligomercounter</a></td>
242 <td>Counts the number of given oligomers in a sequence</td>
243 </tr><tr>
244 <td><a href="gsignature.html">gsignature</a></td>
245 <td>Calculate oligonucleotide usage (genomic signature)</td>
246 </tr>
247
248 </table>
249
250 <h2>Author(s)</h2>
251
252 <pre>
253 Hidetoshi Itaya (celery@g-language.org)
254 Institute for Advanced Biosciences, Keio University
255 252-0882 Japan
256
257 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
258 Institute for Advanced Biosciences, Keio University
259 252-0882 Japan</pre>
260
261 <h2>History</h2>
262
263 2012 - Written by Hidetoshi Itaya
264
265 <h2>Target users</h2>
266
267 This program is intended to be used by everyone and everything, from
268 naive users to embedded scrips.
269
270 <h2>Comments</h2>
271
272 None.
273
274 </BODY>
275 </HTML>