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1 <!--START OF HEADER - DON'T ALTER -->
2
3 <HTML>
4 <HEAD>
5 <TITLE> EMBOSS: greporiter </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 greporiter
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 Get the positions of replication origin and terminus
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 greporiter returns the positions of replication origin and terminus<br />
45 in bacterial genomes by several means. <br />
46 <br />
47 1. Use of databases<br />
48 By default, grep_ori_ter tries to retrieve the position of replication<br />
49 origin in DoriC Gao and Zhang (2007) database, and the position of<br />
50 replication terminus from the supplemental data provided in<br />
51 Kono et al. (2011).<br />
52 If the position of origin cannot be found in the database, but "rep_origin" <br />
53 feature is available, center position within this feature is used for<br />
54 origin. <br />
55 <br />
56 2. Oriloc<br />
57 Using -orilocoption, you can predict the replication origin and <br />
58 terminus using the popular Oriloc program developed by Lobry et al. <br />
59 available as part of the SeqinR package Frank and Lobry (2000).<br />
60 <br />
61 3. Use GC skew shift-point<br />
62 If the positions of origin or terminus cannot be found in the databases,<br />
63 grep_ori_ter automatically calls find_ori_ter() method to predict the <br />
64 positions using GC skew shift-points at one-base-pair resolution.<br />
65 <br />
66 G-language SOAP service is provided by the<br />
67 Institute for Advanced Biosciences, Keio University.<br />
68 The original web service is located at the following URL:<br />
69 <br />
70 http://www.g-language.org/wiki/soap<br />
71 <br />
72 WSDL(RPC/Encoded) file is located at:<br />
73 <br />
74 http://soap.g-language.org/g-language.wsdl<br />
75 <br />
76 Documentation on G-language Genome Analysis Environment methods are<br />
77 provided at the Document Center<br />
78 <br />
79 http://ws.g-language.org/gdoc/<br />
80 <br />
81
82 </p>
83
84 <H2>Usage</H2>
85
86 Here is a sample session with greporiter
87
88 <table width="90%"><tr><td bgcolor="#CCFFFF"><pre>
89
90 % greporiter refseqn:NC_000913
91 Get the positions of replication origin and terminus
92 Output file [nc_000913.greporiter]:
93
94 </pre></td></tr></table>
95
96 Go to the <a href="#input">input files</a> for this example<br>
97 Go to the <a href="#output">output files</a> for this example<br><br>
98
99 <h2>Command line arguments</h2>
100
101 <table border cellspacing=0 cellpadding=3 bgcolor="#ccccff">
102 <tr bgcolor="#FFFFCC">
103 <th align="left">Qualifier</th>
104 <th align="left">Type</th>
105 <th align="left">Description</th>
106 <th align="left">Allowed values</th>
107 <th align="left">Default</th>
108 </tr>
109
110 <tr bgcolor="#FFFFCC">
111 <th align="left" colspan=5>Standard (Mandatory) qualifiers</th>
112 </tr>
113
114 <tr bgcolor="#FFFFCC">
115 <td>[-sequence]<br>(Parameter 1)</td>
116 <td>seqall</td>
117 <td>Nucleotide sequence(s) filename and optional format, or reference (input USA)</td>
118 <td>Readable sequence(s)</td>
119 <td><b>Required</b></td>
120 </tr>
121
122 <tr bgcolor="#FFFFCC">
123 <td>[-outfile]<br>(Parameter 2)</td>
124 <td>outfile</td>
125 <td>Output file name</td>
126 <td>Output file</td>
127 <td><i>&lt;*&gt;</i>.greporiter</td>
128 </tr>
129
130 <tr bgcolor="#FFFFCC">
131 <th align="left" colspan=5>Additional (Optional) qualifiers</th>
132 </tr>
133
134 <tr>
135 <td colspan=5>(none)</td>
136 </tr>
137
138 <tr bgcolor="#FFFFCC">
139 <th align="left" colspan=5>Advanced (Unprompted) qualifiers</th>
140 </tr>
141
142 <tr bgcolor="#FFFFCC">
143 <td>-oriloc</td>
144 <td>boolean</td>
145 <td>Include Oriloc for prediction</td>
146 <td>Boolean value Yes/No</td>
147 <td>No</td>
148 </tr>
149
150 <tr bgcolor="#FFFFCC">
151 <td>-gcskew</td>
152 <td>boolean</td>
153 <td>Include to use GC skew shift-point for prediction</td>
154 <td>Boolean value Yes/No</td>
155 <td>No</td>
156 </tr>
157
158 <tr bgcolor="#FFFFCC">
159 <td>-difthreshold</td>
160 <td>integer</td>
161 <td>Distance between the GC skew shift point and predicted dif site expressed as the precentage of genome size, used as a threshold to retrieve dif sequence from the database</td>
162 <td>Any integer value</td>
163 <td>0</td>
164 </tr>
165
166 <tr bgcolor="#FFFFCC">
167 <td>-dbonly</td>
168 <td>boolean</td>
169 <td>Include to only use values available in databases and to suppress prediction</td>
170 <td>Boolean value Yes/No</td>
171 <td>No</td>
172 </tr>
173
174 <tr bgcolor="#FFFFCC">
175 <td>-[no]accid</td>
176 <td>boolean</td>
177 <td>Include to use sequence accession ID as query</td>
178 <td>Boolean value Yes/No</td>
179 <td>Yes</td>
180 </tr>
181
182 </table>
183
184
185 <h2 id="input">Input file format</h2>
186
187 <p>
188 The database definitions for following commands are available at<br />
189 http://soap.g-language.org/kbws/embossrc<br />
190 <br />
191 greporiter reads one or more nucleotide sequences.<br />
192 <br />
193
194 </p>
195
196 <h2 id="output">Output file format</h2>
197
198 <p>
199 The output from greporiter is to a plain text file.<br />
200 <br />
201 File: nc_000913.greporiter<br />
202 <br />
203 <table width="90%"><tr><td bgcolor="#CCFFCC">
204 Sequence: NC_000913 Origin: 3923881 Terminus: 1550412<br />
205 </td></tr></table>
206
207 </p>
208
209 <h2>Data files</h2>
210
211 <p>
212 None.
213 </p>
214
215 <h2>Notes</h2>
216
217 <p>
218 None.
219 </p>
220
221 <h2>References</h2>
222
223 <pre>
224 Gao F and Zhang CT (2007) DoriC: a database of oriC regions in bacterial
225 genomes, Bioinformatics, 23(14):1866-1867
226
227 Kono N et al. (2011) Comprehensive prediction of chromosome dimer resolution
228 sites in bacterial genomes, BMC Genomics, 12(1):19
229
230 Frank AC and Lobry JR (2000) "Oriloc: prediction of replication boundaries
231 in unannotated bacterial chromosomes", Bioinformatics, 16(6):560-561
232
233 Arakawa, K., Mori, K., Ikeda, K., Matsuzaki, T., Konayashi, Y., and
234 Tomita, M. (2003) G-language Genome Analysis Environment: A Workbench
235 for Nucleotide Sequence Data Mining, Bioinformatics, 19, 305-306.
236
237 Arakawa, K. and Tomita, M. (2006) G-language System as a Platform for
238 large-scale analysis of high-throughput omics data, J. Pest Sci.,
239 31, 7.
240
241 Arakawa, K., Kido, N., Oshita, K., Tomita, M. (2010) G-language Genome
242 Analysis Environment with REST and SOAP Web Service Interfaces,
243 Nucleic Acids Res., 38, W700-W705.
244
245 </pre>
246
247 <h2>Warnings</h2>
248
249 <p>
250 None.
251 </p>
252
253 <h2>Diagnostic Error Messages</h2>
254
255 <p>
256 None.
257 </p>
258
259 <h2>Exit status</h2>
260
261 <p>
262 It always exits with a status of 0.
263 </p>
264
265 <h2>Known bugs</h2>
266
267 <p>
268 None.
269 </p>
270
271 <h2>See also</h2>
272
273 <table border cellpadding=4 bgcolor="#FFFFF0"><tr><th>Program name</th>
274 <th>Description</th></tr>
275
276 <tr>
277 <td><a href="gfindoriter.html">gfindoriter</a></td>
278 <td>Predicts the replication origin and terminus in bacterial</td>
279 </tr>
280
281 </table>
282
283 <h2>Author(s)</h2>
284
285 <pre>
286 Hidetoshi Itaya (celery@g-language.org)
287 Institute for Advanced Biosciences, Keio University
288 252-0882 Japan
289
290 Kazuharu Arakawa (gaou@sfc.keio.ac.jp)
291 Institute for Advanced Biosciences, Keio University
292 252-0882 Japan</pre>
293
294 <h2>History</h2>
295
296 2012 - Written by Hidetoshi Itaya
297
298 <h2>Target users</h2>
299
300 This program is intended to be used by everyone and everything, from
301 naive users to embedded scrips.
302
303 <h2>Comments</h2>
304
305 None.
306
307 </BODY>
308 </HTML>