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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: gpalindrome </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 gpalindrome
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 palindrome sequences
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 gpalindrome searches for palindrome sequences in the genome.<br />
45 Search parameters can be changed for more efficient searches, and g-t<br />
46 matching can be specified by passing the "-gtmatch" qualifier.<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 gpalindrome
69
70 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
71
72 % gpalindrome refseqn:NC_000913
73 Searches palindrome sequences
74 Program compseq output file [nc_000913.gpalindrome]:
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>[-outfile]<br>(Parameter 2)</td>
106 <td>outfile</td>
107 <td>Program compseq output file</td>
108 <td>Output file</td>
109 <td><i>&lt;*&gt;</i>.gpalindrome</td>
110 </tr>
111
112 <tr bgcolor="#FFFFCC">
113 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
114 </tr>
115
116 <tr>
117 <td colspan=5>(none)</td>
118 </tr>
119
120 <tr bgcolor="#FFFFCC">
121 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
122 </tr>
123
124 <tr bgcolor="#FFFFCC">
125 <td>-shortest</td>
126 <td>integer</td>
127 <td>Shortest palindrome to search</td>
128 <td>Any integer value</td>
129 <td>4</td>
130 </tr>
131
132 <tr bgcolor="#FFFFCC">
133 <td>-loop</td>
134 <td>integer</td>
135 <td>Longest stem loop to allow</td>
136 <td>Any integer value</td>
137 <td>0</td>
138 </tr>
139
140 <tr bgcolor="#FFFFCC">
141 <td>-gtmatch</td>
142 <td>boolean</td>
143 <td>If 1, allows g-t match</td>
144 <td>Boolean value Yes/No</td>
145 <td>No</td>
146 </tr>
147
148 <tr bgcolor="#FFFFCC">
149 <td>-[no]accid</td>
150 <td>boolean</td>
151 <td>Include to use sequence accession ID as query</td>
152 <td>Boolean value Yes/No</td>
153 <td>Yes</td>
154 </tr>
155
156 </table>
157
158
159 <h2 id="input">Input file format</h2>
160
161 <p>
162 The database definitions for following commands are available at<br />
163 http://soap.g-language.org/kbws/embossrc<br />
164 <br />
165 gpalindrome reads one or more nucleotide sequences.<br />
166 <br />
167
168 </p>
169
170 <h2 id="output">Output file format</h2>
171
172 <p>
173 The output from gpalindrome is to a plain text file.<br />
174 <br />
175 File: nc_000913.gpalindrome<br />
176 <br />
177 <table width="90%"><tr><td bgcolor="#CCFFCC">
178 Sequence: NC_000913<br />
179 Length, start, end, sequence<br />
180 4,16,18,tg ca<br />
181 4,27,29,at at<br />
182 4,44,46,tt aa<br />
183 4,67,69,ag ct<br />
184 4,97,99,aa tt<br />
185 4,99,101,tt aa<br />
186 10,100,108,taaaa tttta<br />
187 4,132,134,tt aa<br />
188 <br />
189 <font color=red>[Part of this file has been deleted for brevity]</font><br />
190 <br />
191 4,4639484,4639486,tg ca<br />
192 6,4639487,4639491,aag ctt<br />
193 4,4639495,4639497,cg cg<br />
194 4,4639506,4639508,ca tg<br />
195 6,4639552,4639556,gtc gac<br />
196 4,4639607,4639609,tg ca<br />
197 4,4639619,4639621,tg ca<br />
198 4,4639621,4639623,ca tg<br />
199 4,4639625,4639627,at at<br />
200 4,4639637,4639639,at at<br />
201 </td></tr></table>
202
203 </p>
204
205 <h2>Data files</h2>
206
207 <p>
208 None.
209 </p>
210
211 <h2>Notes</h2>
212
213 <p>
214 None.
215 </p>
216
217 <h2>References</h2>
218
219 <pre>
220 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
221 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
222 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
223
224 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
225 large-scale analysis of high-throughput omics data, J. Pest Sci.,
226 31, 7.
227
228 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
229 Analysis Environment with REST and SOAP Web Service Interfaces,
230 Nucleic Acids Res., 38, W700-W705.
231
232 </pre>
233
234 <h2>Warnings</h2>
235
236 <p>
237 None.
238 </p>
239
240 <h2>Diagnostic Error Messages</h2>
241
242 <p>
243 None.
244 </p>
245
246 <h2>Exit status</h2>
247
248 <p>
249 It always exits with a status of 0.
250 </p>
251
252 <h2>Known bugs</h2>
253
254 <p>
255 None.
256 </p>
257
258 <h2>See also</h2>
259
260 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
261 <th>Description</th></tr>
262
263 <tr>
264 <td><a href="gconsensusz.html">gconsensusz</a></td>
265 <td>Calculate consensus in given array of sequences</td>
266 </tr><tr>
267 <td><a href="gdistincc.html">gdistincc</a></td>
268 <td>Calculates the distance between two loci in circular chromosomes</td>
269 </tr><tr>
270 <td><a href="gseqinfo.html">gseqinfo</a></td>
271 <td>Prints out basic nucleotide sequence statistics</td>
272 </tr>
273
274 </table>
275
276 <h2>Author(s)</h2>
277
278 <pre>
279 Hidetoshi Itaya (celery@g-language.org)
280 Institute for Advanced Biosciences, Keio University
281 252-0882 Japan
282
283 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
284 Institute for Advanced Biosciences, Keio University
285 252-0882 Japan</pre>
286
287 <h2>History</h2>
288
289 2012 - Written by Hidetoshi Itaya
290
291 <h2>Target users</h2>
292
293 This program is intended to be used by everyone and everything, from
294 naive users to embedded scrips.
295
296 <h2>Comments</h2>
297
298 None.
299
300